Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30066 discussions

Freeview output viewing error
by Byripudi Naveen Kumar ed20d402 23 Aug '23

23 Aug '23

External Email - Use Caution Dear experts, I'm trying to use freeview to analyse the freeview outputs. I am able to load all the surfaces and volumes onto freeview but I can't see anything on the viewing planes in all 3 slices and 3d views. I have tried to install freesurfer on a completely new device and still the problem persists. I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, I've attached the screenshot of freeview window for reference Hope you could help me resolve this. 1. FreeSurfer version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 2. Platform: Ubuntu 22.04.2 LTS (code name jammy) 3. uname -a Linux Navi 5.15.90.1-microsoft-standard-WSL2 #1 SMP Fri Jan 27 02:56:13 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux 4. Freeview window screenshot attached Thank you Naveen Kumar IIT Madras [image: image.png]

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Spurious BOLD activations along the edge of an oblique partial volume
by Itzik Norman 22 Aug '23

22 Aug '23

External Email - Use Caution Dear FreeSurfer team, I'm using fsfast to analyze 1.2mm^3 7T BOLD data collected with a partial coverage over the hippocampus and superior temporal lobe. I ran preprocessing with the following flags: preproc-sess -d /functional-data -s SUB01 -fsd bold -surface SUB01 lhrh -fwhm 2 -init-header -bbr-int /functional-data/SUB04/bold mT2_WB -per-session And then I ran the GLM analysis (stimulus-vs-baseline) using selxavg3-sess, keeping the data in the subject's native space (using the '-native' flag combined with '-per-session'). The resulting t-map shows a diagonal line of spurious activation along the edge of the functional volume. Is there a way to eliminate this artifact? (see figures attached) Moreover, is there a way to use the -native flag together with -per-run? I want to simultaneously measure the hippocampal activation (in native space) and cortical activity smoothed on the surface; but I want all the data to be processed the same way (-per-run), and currently the volume analysis forces me to use -per-session. I haven't encountered any previously documented issues similar to this one. Please let me know if you have any thoughts. 1) FreeSurfer build stamp: freesurfer-darwin-macOS-7.3.2-20220804-6354275 2) Platform: Mac Studio M1 (macOS) 3) selxavg3-sess log: attached 4) analysis config file: attached Thanks, Itzik [image: image2.png][image: image3.png][image: image1.png]

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Job Position: Postdoc Research Associate at the Center for Healthy Minds
by Center for Healthy Minds Human Resources 22 Aug '23

22 Aug '23

External Email - Use Caution The Center for Healthy Minds at the University of Wisconsin–Madison<https://secure-web.cisco.com/1alZdwyt9ShUTl9SUEacJ-4HTHzY4BrOzC7GyTMTJZ7g0n…> is seeking multiple highly motivated postdoctoral researchers to work on intervention studies in U.S. adults to promote wellbeing and prevent suicide. Areas of research include the evaluation and mechanistic examination of behavioral and physiological interventions in healthy and distressed adults using multiple types of MRI, passive measures of behavior and physiology, and survey measurements. The postdoctoral research associates will have opportunities to participate in activities related to neuroimaging methods development and evaluation, study data collection and analyses, research publications, grant writing and are expected to make positive scholarly contributions to this interdisciplinary and highly collaborative research program. Qualifications: Required Ph.D. in medical physics, psychology, neuroscience, and/or a related field Prior experience with brain imaging techniques (e.g. MRI, DTI, and/or fMRI) and/or behavioral data Strong communication and organization skills are a must. Preferred Experience with brain image analysis software tools, MATLAB, Python, C++ and/or other computer programming (e.g., R, Mplus) Experience with large and complex research studies and/or clinical trials Emerging track record of publishing in academic journals, strong analytic skills, and excel at working in a collaborative environment. We are an equal opportunity/affirmative action employer. We promote excellence through diversity and encourage all qualified individuals to apply. To view the full posting with application instructions please go to https://secure-web.cisco.com/1VdOrlXBZlLhFv9xXJTvkxUg9UcYvjBez8PJM194TBa2Rz…

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Password for unzipping Virtual Box Image file
by mkassinopoulos＠barcelonabeta.org 22 Aug '23

22 Aug '23

External Email - Use Caution Hi, I would like to request the passcode for unzipping the Virtual Box Image file (i.e. FS_7_2_0_ubuntu_18_04_06.ova.7z). Best regards, Michalis

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[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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