Freesurfer April 2021

freesurfer@nmr.mgh.harvard.edu

104 participants
144 discussions

Parcellation Error Pre-Post Central Gyrus R but not L Hemisphere
by Fraser Smith 26 Apr '21

26 Apr '21

External Email - Use Caution Hi there I have a clear parcellation error with one participant who does look to have an atypical structure around the right post-central gyrus (looks split in two). Both the pre and post central gyri are shifted significantly backwards – but only for the right not the left hemisphere. I see this has been mentioned before in the archives – but I have been unable to find a fix for this. Could you provide any tips on what to try? I am using v6.0.0. Best wishes Fraser Smith

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aseg+ striatum parcellation_choi'2012
by Laila Khedher-Brahim 26 Apr '21

26 Apr '21

External Email - Use Caution Hi, after the transformation of the Choi's striatal 2012 to the individual subject, I would like to do the segmentation + the striatum parcellation_Choi2012. How I can do that in order to have in the end the aseg + aparc.mgz file in order to have the volume of this ROI. Cordially, Laila Laila Khedher Brahim Docteur en technologies d'information et de communication- Traitement des données laila.khedher-brahim(a)inra.fr Laboratoire Neuro-psychopharmacologie des systèmes dopaminergiques sous-corticaux (Facultés de Médecine et de Pharmacie) && Plateforme AgroResonance (https://secure-web.cisco.com/11FFmmQRyEScyxQhBuoUqIhMH3n21rZigLqcx-nZj13jlG…) Tel: +33 (0)4 73 62 4177

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T2 lesion editing
by AJ 26 Apr '21

26 Apr '21

External Email - Use Caution Hi, Once SAMSEG has finished segmenting T2 lesions, other than trying different --threshold flags, any way to manually modify them? Can --eTIV be added to SAMSEG? In Samseg, can brainstem be segmented into parts, such as medulla, pons, mid brain like through recon all? Can corpus callosum be segmented separately in Samseg? Sorry for all the questions. Many thanks.

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glm_fit Contrast
by Boa Sorte Silva, Narlon 26 Apr '21

26 Apr '21

External Email - Use Caution Dear FS experts, Hope this finds you well. I would like to check whether the following the correct approach for my models in glm_fit. I am testing whether gait speed is associated with cortical thickness, adjusting for 4 covariates (sex, age, bmi, and mmse). I have sex as a factor (two levels: male or female), age, bmi, and mmse are continuous variables. Thus, the FSGD file is ordered as: subj_id sex gait age bmi mmse In the models, I am using DOSS with the following contrast: [+0 +0 +1 +0 +0 +0] I would appreciate your kind input as to whether the above design and contrast is the proper way to test my research question. Thank you very much for your help. Best regards, Nárlon Cassio Nárlon Cássio Boa Sorte Silva PhD (He, Him, His) CIHR/MSFHR Postdoctoral Research Fellow Aging, Mobility, and Cognitive Neuroscience Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy, Faculty of Medicine University of British Columbia Vancouver, Canada Twitter: @BoaNarlon [X]

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Trying to highlight insula
by Kelli Ann Nini 25 Apr '21

25 Apr '21

External Email - Use Caution Greetings esteemed surfers, I am trying to take an image of the insula using the LUT. I've loaded volumes T1, wm, brainmask, and aseg respectively, and checked all three views but for some reason labels 19 and 55 (Left & Right Insula) "does not exist in volume". Thank you in advance! -Kelli NOTICE: This message, including all attachments transmitted with it, is intended solely for the use of the Addressee(s) and may contain information that is PRIVILEGED, CONFIDENTIAL, and/or EXEMPT FROM DISCLOSURE under applicable law. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution, or use of the information contained herein is STRICTLY PROHIBITED. If you received this communication in error, please destroy all copies of the message, whether in electronic or hard copy format, as well as attachments and immediately contact the sender by replying to this email or contact the sender at the telephone numbers listed above. Thank you!

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asegstats2table: Cannot find stats file
by Haneen Hakeem 25 Apr '21

25 Apr '21

External Email - Use Caution Hello FreeSurfer Developers, I’m attempting to output stat files using “asegstats2table” and “aparcstats2table” but for some of my subjects I get the following error when I run the commands: ERROR: Cannot find stats file /apps/freesurfer/7.0.0/freesurfer/subjects/APC011/stats/aseg.stats However, when I check the stats file in FreeSurfer output directory, the stats files are there (including asset.stats). This issue is recurring with all “asegstats2table” and “aparcstats2table” stat files. 1) freesurfer version FreeSurfer 7.0 2) Platform: Bash remotely through High Performance Computing (HPC) on a MacOS Mojave 3) recon all log attached

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mri_glmfit FIR model
by Marilena Wilding 25 Apr '21

25 Apr '21

External Email - Use Caution Dear Freesurfers, I’m currently doing 2nd level analysis on a FIR model. I first concatenated my data with this command: isxconcat-sess -sf sessidlist -analysis FIR_group.lh -contrast global-v-local -no-hrf -hemi lh -o group_analysis I got 29 timepoints and their corresponding 29 ces.nii and cesvar.nii files. Then I ran glmfit (for each timepoint): mri_glmfit \ --y ces.000.nii \ --wls cesvar.000.nii.gz \ --surface fsaverage lh \ --glmdir group_GLM_lh_000.wls \ --osgm \ --nii.gz In my paradigm I’m showing a stimulus that can be seen in two ways. In my analysis I separate the runs, depending on what the participant indicated to have seen (1 or 2) and compute the contrast in activation between these two percepts. I was now wondering if the command above is correct with the ‘osgm’-flag? Since I’m only interested in the difference between the two conditions from the paradigm and not different groups of participants (e.g. patients vs. healthy people) I don’t have to specify a fsgd file, correct? And if I wanted to specify covariates I’d just make such a file but without groups and only variables? Thank you very much for your help! Best, Mara

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mri_convert error for creating flat_lh.gii file
by Suzanne Nie 25 Apr '21

25 Apr '21

External Email - Use Caution Hello Freesurfer Developers, I'm attempting to create a full surfaces folder in the filestore based on the example, with flat_lh.gii, inflated_lh.gii, pia_lh.gii, wm_lh.gii, and those for the right hemisphere in order to use cortex.quickshow, plt.show, and cortex.webgl.show. I used cortex.freesurfer.flatten to create files lh.full.flat.patch.3d and rh.full.flat.patch.3d from lh.full.patch.3d that I created from making cuts. I want to convert these files to flat_lh.gii, but mris_conver gives me segmentation fault errors. mris_convert lh.full.flat.patch.3d flat_lh.gii ASSERTION FAILED: /Users/developer/space_freesurfer/build/tulum/trunk/developer-7.1.1/utils/mrisurf_metricProperties.cpp:4323 mris->dist_nsize == 0 ASSERTION FAILED: /Users/developer/space_freesurfer/build/tulum/trunk/developer-7.1.1/utils/mrisurf_metricProperties.cpp:4323 mris->dist_nsize == 0 Segmentation fault: 11 I was unable to find similar issues. If my goal is to display using cortex.webgl.show, is creating these files the correct step and if so, are there any instructions explaining possible steps? - Freesurfer Version: freesurfer-darwin-macOS-7.1.1-20200811-8b40551 - Platform: macOS Catalina Version 10.15.7 - Darwin Suzannes-MBP 19.6.0 Darwin Kernel Version 19.6.0: Mon Aug 31 22:12:52 PDT 2020; root:xnu-6153.141.2~1/RELEASE_X86_64 x86_64 - recon-all.log attached Thank you, Suzanne

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Hipppocampal segmentation on freesurfer
by Jindal, Saurabh 25 Apr '21

25 Apr '21

External Email - Use Caution Hi experts, I am working on freesurfer 7.1 now and my ROI is hippocampus, but it seems that there is some non-hippocampal inclusion in the form of choroid plexus and adjacent peri-ventricular white matter. Do we have a standard cutoff criterion for hippocampal inclusion? Like how many voxels for how many slices is okay to let it pass? Saurabh ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Hippocampus segmentHA_T1.sh
by Wei Shao 23 Apr '21

23 Apr '21

External Email - Use Caution Hello, Dear FreeSurfer expert I tried to use segmentHA_T1.sh for the hippocampus subfields, However, here is the log cannot find the wmparc.mgz or norm.mgz or talairach.xfm for the subject. Has the subject been procesed with recon-all? But the wmparc.mgz and norm.mgz are there [image: Capture.PNG] Could you tell me how to fix this? Thanks! Best, Wei

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Freesurfer April 2021