preclinical data

Question

preclinical data

IRISstrasbourg opened this issue 5 years ago · 19 comments

Hello,

I'm working in Strasbourg (France) on Bruker system. I did MP2RAGE acquisition which I would like process using your code.
Installation was easy helped by your clear instructions.
I meet issue with -acqparam. In preclinical, we don't used parallel imaging, so, no GRAPPA.
Which option do I must write in -acqparam?
My actual command line, which is not perfect because didn't take in account the absence of GRAPPA, is:
python /mnt/hgfs/share/logiciels/mp2rage-master/mp2rage_compute_t1_map.py -i MP2RAGE.nii -acqparam ti=800,2200:alpha=7,7:tr_seq=6250:tr_gre=8.74:matrix_sizes=128,128,128:bandwidths=20000,20000 -t1range 100,5000 -o T1map.nii.gz,RHOmap.nii.gz

Message after process:
Sequence parameters:
({'tr_gre': 8.74, 'n_gre': 96, 'a1': 7.0, 'a2': 7.0, 'tb': 480.96000000000004, 'tc': 3525.6, 'eff': 0.95, 'ta': 565.36}, {'t_acq': 500.0})
Traceback (most recent call last):
File "/mnt/hgfs/share/logiciels/mp2rage-master/mp2rage_compute_t1_map.py", line 210, in
main()
File "/mnt/hgfs/share/logiciels/mp2rage-master/mp2rage_compute_t1_map.py", line 139, in main
T1map_data, RHOmap_out_data = pmc.t1_mp2rage(rho_arr=rho.get_data(), t1_value_range=t1range, **acq_params)
File "/home/po/.local/lib/python2.7/site-packages/pymrt/computation.py", line 597, in t1_mp2rage
if rho_arr == None:
ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()

Thank you,
Chrystelle

Answer 1 · 2019-08-09T03:16:06.000Z

hi Chrystelle,

sorry for the late response. Without having the data, it is difficult to know what causes the bug (is it a problem in the input data?). Are you able to debug this by yourself by running the code in debug mode (e.g. using an IDE like Pycharm) and look at your problematic variable rho_arr before it crashes? If not maybe you can send you the data and we can look at it ourself

best,
Julien

Answer 2 · 2019-08-26T09:04:07.000Z

Hello,

I don't have the good soft to run it in debug mode.
I will send you by email the raw data if it's fine for you.

Best,
Chrystelle

Answer 3 · 2019-08-28T11:41:08.000Z

Hi Chrystelle,
OK this is fine, you can email me the data and we will look into it.

Answer 4 · 2019-08-28T12:06:03.000Z

Hello, My previous email (below) never arrived. Damned! Thank you for your help, Chrystelle

…

-------- Message transféré -------- Sujet : Re: [neuropoly/mp2rage] preclinical data (#2) Date : Mon, 26 Aug 2019 11:23:48 +0200 De : Chrystelle Po <po@unistra.fr> Pour : Julien Cohen-Adad <notifications@github.com> Bonjour Julien, Je me permets de te répondre en français. Désolée pour ma réponse tardive. Je reviens de vacances. Si tu es toujours d'accord,tu trouveras un jeu de donnée acquis sur une souris en format nifti sur le lien suivant: https://seafile.unistra.fr/f/019669a159c648528447/?dl=1 Il s'agit d'une hyperstack composée des deux TI (800 et 2200 ms), 64 coupes. Tu y trouveras aussi les documents method et reco créés par Bruker lors de l'acquisition où se trouvent une partie des paramètres. Mais voici les autres principaux paramètres: TR: 6250 tr_ge: 8.744 matrix: 128 x 128x 64 (me suis plantée sur la ligne de code mais pas plus de réussite en mettant la bonne valeur) impulsions: 7,7 bandwidth: 20000, 20000 N'hésite pas à me contacter si jamais j'ai oublié une information. Un grand merci pour ton aide, A bientôt, Chrystelle Le 09/08/2019 à 05:16, Julien Cohen-Adad a écrit :

hi Chrystelle, sorry for the late response. Without having the data, it is difficult to know what causes the bug (is it a problem in the input data?). Are you able to debug this by yourself by running the code in debug mode (e.g. using an IDE like Pycharm) and look at your problematic variable |rho_arr| before it crashes? If not maybe you can send you the data and we can look at it ourself best, Julien — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#2?email_source=notifications&email_token=AM2ULFNAHLWNKLRMFVTXT5LQDTOPRA5CNFSM4IJWHKW2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD35O5MI#issuecomment-519761585>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AM2ULFOMLDD45KPBBVCQJEDQDTOPRANCNFSM4IJWHKWQ>.

-- ------------------------------------------------------------------------------------ Chrystelle PO, Ph.D. Ingénieur de Recherche CNRS / Research scientist CNRS Equipe IMIS/Plateforme IRIS Laboratoire des sciences de l’Ingénieur, de l’Informatique et de l’Imagerie (ICube) Université de Strasbourg - CNRS Adresse postale / Mailing address : Institut de Physique Biologique, Faculté de Médecine 4, rue Kirschleger, 67085 STRASBOURG CEDEX Tél : +33 (0)3.68.85.40.76 Plateforme IRIS:http://plateforme.icube.unistra.fr/iris/index.php/Accueil laboratoire ICube:https://icube.unistra.fr/ ------------------------------------------------------------------------------------

Answer 5 · 2019-08-29T15:20:40.000Z

I get the same error message. I replaced if rho_arr == None: on line 597 to if rho_arr is None: and now it works.

Answer 6 · 2019-08-29T15:22:37.000Z

thank you very much @devDonnn

Answer 7 · 2019-08-29T15:22:41.000Z

Cool! It looks simple solution! Thank you so much, I will test it tomorrow. Le 29/08/2019 à 17:20, Donatas Sederevicius a écrit :

…

I get the same error message. I replaced |if rho_arr == None:| on line 597 to |if rho_arr is None:| and now it works. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#2?email_source=notifications&email_token=AM2ULFKWY6ACW4D6F42TVT3QG7SMRA5CNFSM4IJWHKW2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD5O3HTQ#issuecomment-526234574>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AM2ULFPEX2G64BXMI4ZXUPTQG7SMRANCNFSM4IJWHKWQ>.

Answer 8 · 2019-08-29T18:51:15.000Z

Cool! @IRISstrasbourg please let us know if this works for you and resolves all your issues.

Answer 9 · 2019-08-30T07:36:12.000Z

Hello, I changed computation.py as devDonnn suggestedand then, I used this command line: /python /mnt/hgfs/share/logiciels/mp2rage-master/mp2rage_compute_t1_map.py -i MP2RAGE_TI1-800_souris1-19.nii -acqparam ti=800,2200:alpha=7,7:tr_seq=6250:tr_gre=8.744:matrix_sizes=128,128,64:bandwidths=20000,20000:grappa_factors=1,1,1:grappa_refs:0,0,0 -t1range 100,5000 -o T1map.nii.gz,RHOmap.nii.gz/ I get this new message :( /Traceback (most recent call last):// // File "/mnt/hgfs/share/logiciels/mp2rage-master/mp2rage_compute_t1_map.py", line 210, in <module>// // main()// // File "/mnt/hgfs/share/logiciels/mp2rage-master/mp2rage_compute_t1_map.py", line 105, in main// // acq_param.update(paramKey)// // File "/mnt/hgfs/share/logiciels/mp2rage-master/mp2rage_compute_t1_map.py", line 78, in update// // list_val = list_key_val[1].split(',')// //IndexError: list index out of range/ Do you have an idea to solve it? Thank you Le 29/08/2019 à 20:51, Mathieu Boudreau a écrit :

…

Cool! @IRISstrasbourg <https://github.com/IRISstrasbourg> please let us know if this works for you and resolves all your issues. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2?email_source=notifications&email_token=AM2ULFIBJI7VTQPKE5TBILLQHALCHA5CNFSM4IJWHKW2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD5PO3RQ#issuecomment-526314950>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AM2ULFKQNQ4XYOIZXBWWZ5LQHALCHANCNFSM4IJWHKWQ>.

Answer 10 · 2019-08-31T02:45:11.000Z

@IRISstrasbourg you made mistake in the command. Change grappa_refs:0,0,0to grappa_refs=0,0,0.

Answer 11 · 2019-09-02T07:18:15.000Z

Pfff, so stupid error :/
But there is still following message error:
Sequence parameters:
({'tr_gre': 8.744, 'n_gre': 48, 'a1': 7.0, 'a2': 7.0, 'tb': 980.288, 'tc': 3787.68, 'eff': 0.95, 'ta': 642.608}, {'t_acq': 800.0})
Traceback (most recent call last):
File "/mnt/hgfs/share/logiciels/mp2rage-master/mp2rage_compute_t1_map.py", line 210, in
main()
File "/mnt/hgfs/share/logiciels/mp2rage-master/mp2rage_compute_t1_map.py", line 139, in main
T1map_data, RHOmap_out_data = pmc.t1_mp2rage(rho_arr=rho.get_data(), t1_value_range=t1range, **acq_params)
File "/home/po/.local/lib/python2.7/site-packages/pymrt/computation.py", line 597, in t1_mp2rage
if rho_arr == None:
ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()

It seems I have a parameters error somewhere but I checked in Bruker raw data each one.

Answer 12 · 2019-09-02T11:51:40.000Z

Have you actually changed the code on line 597 in computation.py script? It seems you are getting the same error as the first time.

Answer 13 · 2019-09-02T11:57:24.000Z

Yes. I did it. I leave the previous command as comment in the script. /# if rho_arr == None:// // if rho_arr is None:/ Le 02/09/2019 à 13:51, Donatas Sederevicius a écrit :

…

Have you actually changed the code on line 597 in computation.py script? It seems you are getting the same error as the first time. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2?email_source=notifications&email_token=AM2ULFOOLON5MOF2MZNS7RLQHT44ZA5CNFSM4IJWHKW2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD5VTHSQ#issuecomment-527119306>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AM2ULFIYBRIOYYT7YMFYVC3QHT44ZANCNFSM4IJWHKWQ>.

Answer 14 · 2019-09-02T12:41:26.000Z

@IRISstrasbourg Can you update computation.py script here: home/po/.local/lib/python2.7/site-packages/pymrt/computation.py? It seems that your previous edit is not taking effect as computation.py is read from home/po/.local/lib/python2.7/site-packages/pymrt/ not /mnt/hgfs/share/logiciels/mp2rage-master/.

Answer 15 · 2019-09-02T13:13:44.000Z

I changed the computation.py script localized in home/po/.local/lib/python2.7/site-packages/pymrt/.
New message :'(
Traceback (most recent call last):
File "/mnt/hgfs/share/logiciels/mp2rage-master/mp2rage_compute_t1_map.py", line 17, in
import pymrt.computation as pmc
File "/home/po/.local/lib/python2.7/site-packages/pymrt/computation.py", line 600
else:
^
IndentationError: unindent does not match any outer indentation level

Answer 16 · 2019-09-02T13:25:07.000Z

It means that your newly updated if statement is not in the same alignment with its corresponding else statement. Check how many spaces you have before **if** starts and then how many spaces before **else**. Make the same number of spaces before each.

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Sent from my iPhone

On 2 Sep 2019, at 09:13, IRISstrasbourg ***@***.***> wrote: I changed the computation.py script localized in home/po/.local/lib/python2.7/site-packages/pymrt/. New message :'( Traceback (most recent call last): File "/mnt/hgfs/share/logiciels/mp2rage-master/mp2rage_compute_t1_map.py", line 17, in import pymrt.computation as pmc File "/home/po/.local/lib/python2.7/site-packages/pymrt/computation.py", line 600 else: ^ IndentationError: unindent does not match any outer indentation level — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

Answer 17 · 2019-09-02T13:39:38.000Z

It's working and I need to learn python language ;)

Thank you so much!!!!

Answer 18 · 2019-09-10T14:14:11.000Z

@IRISstrasbourg could you confirm again that the your issue running this software with your data has been resolved?

If so, I think we could do the suggested fix by:

I get the same error message. I replaced if rho_arr == None: on line 597 to if rho_arr is None: and now it works.

and merge it to master so that all users can benefit from this fix.

Answer 19 · 2019-09-10T14:28:37.000Z

Hello, Yes. The software is running properly now. Thank you again. Le 10/09/2019 à 16:14, Mathieu Boudreau a écrit :

…

@IRISstrasbourg <https://github.com/IRISstrasbourg> could you confirm again that the your issue running this software with your data has been resolved? If so, I think we could do the suggested fix by: I get the same error message. I replaced |if rho_arr == None:| on line 597 to |if rho_arr is None:| and now it works. and merge it to master so that all users can benefit from this fix. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2?email_source=notifications&email_token=AM2ULFMCSQIPNQATWSFO5CTQI6TTJA5CNFSM4IJWHKW2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6LHTXI#issuecomment-529955293>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AM2ULFNDMBTHJXRHUDHU2E3QI6TTJANCNFSM4IJWHKWQ>.