Freesurfer August 2023

freesurfer@nmr.mgh.harvard.edu

89 participants
126 discussions

[FreeSurfer] ValueError axes don't match array
by Krystal Xiwing Yau 22 Aug '23

22 Aug '23

External Email - Use Caution Dear FreeSurfer experts, I have completed the processes of coregistration of FLAIR to T1 image for the subject. As I ran samseg with lesion contrast, the following error message occurred: writing template transform to /home/admin1/freesurfer/subjects/103_samsegOutput/template.lta writing talairach transform to /home/admin1/freesurfer/subjects/103_samsegOutput/samseg.talairach.lta atlas registration complete: 0:00:17.614971 /home/admin1/freesurfer/python/lib/python3.8/site-packages/numpy/core/_asarray.py:83: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray return array(a, dtype, copy=False, order=order) Traceback (most recent call last): File "/home/admin1/freesurfer/python/scripts/run_samseg", line 190, in <module> _, _, _, optimizationSummary = samseg.segment( File "/home/admin1/freesurfer/python/packages/freesurfer/samseg/Samseg.py", line 255, in segment self.preProcess() File "/home/admin1/freesurfer/python/packages/freesurfer/samseg/Samseg.py", line 318, in preProcess self.imageBuffers, self.transform, self.voxelSpacing, self.cropping = readCroppedImages( File "/home/admin1/freesurfer/python/packages/freesurfer/samseg/SamsegUtility.py", line 139, in readCroppedImages croppedImageBuffers = np.transpose(croppedImageBuffers, axes=[1, 2, 3, 0]) File "<__array_function__ internals>", line 5, in transpose File "/home/admin1/freesurfer/python/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 653, in transpose return _wrapfunc(a, 'transpose', axes) File "/home/admin1/freesurfer/python/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 55, in _wrapfunc return _wrapit(obj, method, *args, **kwds) File "/home/admin1/freesurfer/python/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 44, in _wrapit result = getattr(asarray(obj), method)(*args, **kwds) ValueError: axes don't match array Would somebody be kindly advise? Thank you. Regards, Krystal Tel.: +852 2255 5024 Fax: +852 2872 5828 Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.

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(no subject)
by 林耀云 21 Aug '23

21 Aug '23

External Email - Use Caution Hi Freesurfer Team, I have a question can’t understand. Why just uses general linear model to analysis in Freesurfer? There are a lot of models such as nonlinear model, SVM and others. Please help me answer. Thank you so much. Additionally, as attached picture, Do we need to transform all the data to the coronal plane? Can’t be a sagittal and axial plane? Thanks so much! Best, Yaoyun

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Help running freesurfer for FEAT-preprocessed functional data?
by Noah Lee 21 Aug '23

21 Aug '23

External Email - Use Caution Hello! I am trying to run some freesurfer commands for a pipeline. However, I am coming in with functional data preprocessed by FEAT (EPI correction and general mcflirt, etc). For reference, I'm trying to run this following script: preproc-sess -s . -fwhm 5 -stc siemens -surface fsaverage lhrh -per-run -fsd bold -mni305 -force fcseed-config -wm -fcname wm.dat -fsd bold -mean -cfg wm.config -force fcseed-config -vcsf -fcname vcsf.dat -fsd bold -mean -cfg vcsf.config -force fcseed-sess -s . -cfg wm.config -force fcseed-sess -s . -cfg vcsf.config -force I am obviously skipping the preproc-sess step, as my data has been preprocessed. However, I'm not too sure how to run the following steps with the outputs of my feat directory. If anyone could help, I would greatly appreciate it! Best, Noah Lee he/him/his Yale University | Saybrook '25 B.S. Neuroscience

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Extracting Mean Cortical Thickness from Specific Region
by MANSSOUR Wassima 21 Aug '23

21 Aug '23

External Email - Use Caution Dear FreeSurfer Experts, I am new to FreeSurfer and I need to extract the mean cortical thickness from a specific region for each subject in my dataset (then for my 2 groups). I have already identified a significant cluster from a group analysis, and I would greatly appreciate your guidance on how to proceed with this analysis. >From what I understand, the general steps involve creating a label for the region of interest and then extracting the necessary statistics. Here's what I've tried so far: 1.Created a label for the significant cluster using the mri_cor2label command: mri_cor2label --i lh.moca_all.thickness.glmdir/MOCApos/cache.th20.pos.sig.cluster.mgh --id 1 --l ./cluster_label.label 2.Attempted to extract the statistics using the mris_anatomical_stats command for the HCA6002236_V1_MR subject: mris_anatomical_stats -l cluster_label.label -f parietal_stats1 HCA6002236_V1_MR lh However, the output parietal_stats1 from the mris_anatomical_stats command is empty, and I'm not sure where I might be going wrong. While if I try: mris_anatomical_stats -t lh..moca_all.thickness.glmdir/MOCApos/cache.th13.pos.sig.cluster.mgh -f parietal_stats2 HCA6002236_V1_MR lh I got 0mm in the averge thickness. You find attached the 2 outputs files. Thank you for your help. -- Wassima MANSSOUR Master Student at INSEA Rabat M2SI - Information Systems & Intelligent Systems IMRB Intern -France wmanssour(a)insea.ac.ma<mailto:wmanssour@insea.ac.ma> wassima.manssour(a)u-pec.fr<mailto:wassima.manssour@u-pec.fr>

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[FreeSurfer] recon-edit advice
by Krystal Xiwing Yau 21 Aug '23

21 Aug '23

External Email - Use Caution Dear FreeSurfer experts, It has been a problem for me to fix this kind of issue, and am struggling to obtain the accurate data from it. I tried to edit wm.mgz as well as adding control points in attempt to expand the pial surface all the way up to the gyrus in temporal lobe. However, it only shows a tiny area calculated as pial surface in the right temporal lobe as shown below: [cid:82de6f15-78d4-420c-b293-a123ad12cc38] During the process of autorecon2-cp, I saw a message saying "An extra large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz." May I know where I can spot out the defect? Moreover, does it relate to the quality of images? Thank you. Regards, Krystal Tel.: +852 2255 5024 Fax: +852 2872 5828 Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.

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taskreg with inconsistent regressor number
by wangzhiwei3233 21 Aug '23

21 Aug '23

External Email - Use Caution Dear FreeSurfer experts, In my experiment, some subjects missed some trials and some not. I wish set the missed trials as an external regressor, however, mkanalysis-sess seems applying the same parameters for all subjects. In my understanding, -taskreg extreg N, the N is same for all subjects. Is my understanding right? If it is right, how can I sove my problem that not all subjects have the external regressor because some subjects have no missing trials? Best, Zhiwei

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Re: [Freesurfer] ScLimbic issue
by fsbuild 21 Aug '23

21 Aug '23

External Email - Use Caution  Check if you see the following output for these commands,  % which mri_sclimbic_seg /usr/local/freesurfer/7.4.1/bin/mri_sclimbic_seg % which fspython /usr/local/freesurfer/7.4.1/bin/fspython Try running that command as listed below followed by your own arguments to it, i.e. try, %  bash -x `which mri_sclimbic_seg` --s HAB_008_CST_2.4 .... and send along the output ... - R. On Aug 20, 2023, at 21:31, Jacobs, Heidi I.,PHD <HJACOBS(a)mgh.harvard.edu> wrote:mri_sclimbic_seg 

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Re: [Freesurfer] ScLimbic issue
by fsbuild 20 Aug '23

20 Aug '23

External Email - Use Caution  You should be able to use either of the paths below for FREESURFER_HOME to run the freesurfer CentOS7 7.4.1 release.  You should see the same output using either path.   If one of these commands does not work, then it means that path is not mounted/available on your machine (so don’t use that one). % cat /usr/local/freesurfer/7.4.1/build-stamp.txt  freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 % cat /autofs/cluster/freesurfer/centos7_x86_64/7.4.1/build-stamp.txt  freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 Both commands work on my test machine, so I will use the first one.  Using csh to setup the environment, % setenv FREESURFER_HOME /usr/local/freesurfer/7.4.1 % source $FREESURFER_HOME/SetUpFreeSurfer.csh -------- freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   /usr/local/freesurfer/7.4.1 FSFAST_HOME       /usr/local/freesurfer/7.4.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /usr/local/freesurfer/7.4.1/subjects MNI_DIR           /usr/local/freesurfer/7.4.1/mni FSL_DIR           /usr/pubsw/packages/fsl/current But your posted output from the source command does not match the output above.  It is fine to change SUBJECTS_DIR to a different path *after* you run the “source” command above, in order to process your own data, e.g., % setenv SUBJECTS_DIR /autofs/space/locus_001/users/mv1048/LC_HYP/FS6 I’m wondering if something was added into your shell initialization file in your home directory to set FREESURFER_HOME, etc. to be different.  For csh, that would be your “.cshrc" file..  I would check that file and either change or comment out setting FREESURFER_HOME there, etc.  But you should get the same output listed above from the source command (apart from changing SUBJECTS_DIR). - R. On Aug 20, 2023, at 18:12, Jacobs, Heidi I.,PHD <HJACOBS(a)mgh.harvard.edu> wrote:/autofs/space/locus_001/users/mv1048/LC_HYP/FS6

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Re: [Freesurfer] ScLimbic issue
by fsbuild 20 Aug '23

20 Aug '23

External Email - Use Caution  …. to do that, you can set FREESURFER_HOME to /autofs/cluster/freesurfer/centos7_x86_64/7.4.1On Aug 20, 2023, at 17:52, Douglas N. Greve <dgreve(a)mgh.harvard.edu> wrote:        External Email - Use Caution        Can you try the 7.4.1 version? Can you also send your full command line and terminal output?On 8/20/2023 2:57 PM, Jacobs, Heidi I.,PHD wrote:        External Email - Use Caution        Hello FreeSurfer team, I am trying to run the sclimbic tool on our FreeSurfer processed images (from the Martinos center).For some unknown reason I keep getting the same problem:Excluding seg [853]Using CPUIllegal instruction (core dumped) Not sure what this means?I have sourced /usr/local/freesurfer/nmr-dev-env  and set the SUBJECTS_DIR correctly.I tried with the - - s option referring to the FreeSurfer processed subject as well as the - - i option, referring to the orig.mgz image.Using the nifti image or the mgz image doesn’t make a difference either. Any suggestions on what the problem may be or how to resolve this? Thank youAll the bestHeidi_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/16K48adfKEFhjBEWcGDdxxH9bAWC3bNvVBu3BkyrQV4-vi… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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ScLimbic issue
by Jacobs, Heidi I.,PHD 20 Aug '23

20 Aug '23

External Email - Use Caution Hello FreeSurfer team, I am trying to run the sclimbic tool on our FreeSurfer processed images (from the Martinos center). For some unknown reason I keep getting the same problem: Excluding seg [853] Using CPU Illegal instruction (core dumped) Not sure what this means? I have sourced /usr/local/freesurfer/nmr-dev-env and set the SUBJECTS_DIR correctly. I tried with the - - s option referring to the FreeSurfer processed subject as well as the - - i option, referring to the orig.mgz image. Using the nifti image or the mgz image doesn’t make a difference either. Any suggestions on what the problem may be or how to resolve this? Thank you All the best Heidi

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Freesurfer August 2023