Freesurfer August 2017

freesurfer@nmr.mgh.harvard.edu

145 participants
233 discussions

Error while running recon-all
by Ritesh Mahajan 06 Sep '17

06 Sep '17

Hello guys, I am trying to run recon-all command, i am getting the following error: error while loading shared libraries: libgomp.so.1: cannot open shared object file: No such file or directory Can anyone help me out with this. Thanks, Ritesh Mahajan

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wm topological defects
by Manuel Delgado 06 Sep '17

06 Sep '17

Dear all: Regarding wm edits, it is shown in the tutorial how to proceed with "holes" that appear in the smoothwm.nofix. However, those holes do not necessarily affect the wm matter surface. So is it recommendable to check if holes in the smoothwm.nofix surface affect the real wm surface before correcting them? And, what is the purpose of the smoothwm.nofix, is it used for other issues? Thank you -- *Manuel Delgado Alvarado, MD* *Predoctoral Researcher* *Neuroimaging Unit, IDIVAL* *Avda. Cardenal Herrera Oria s/n* *39011 Santander, Spain*

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rh.white and rh.pial surface manual edit
by Farhad Ghaseminejad 06 Sep '17

06 Sep '17

Hello FreeSurfer experts, I was wondering if you have any suggestions on how to fix the error in the rh.white and rh.pial surface in the Orbitofrontal cortex as shown in the screenshots attached. https://drive.google.com/drive/folders/0B64fNVlVdTBYOVhJMXJyTjZVSTQ?usp=sha… <https://drive.google.com/drive/folders/0B64fNVlVdTBYOVhJMXJyTjZVSTQ?usp=sha…> Best, Farhad

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controlling for Sex in a model using two continuous variables onto CTh
by Uquillas, Federico D'Oleire 05 Sep '17

05 Sep '17

Dear FreeSurfer experts, We have run a vertex-wise analysis regressing a continuous variable onto cortical thickness on the surface, and would like to verify that our contrast that uses Age and Sex as covariates was defined correctly, especially since there is probably more than one way to control for a binary variable like Sex. On the website (https://surfer.nmr.mgh.harvard.edu/fswiki/DodsDoss) it suggests to make two regressors, one for Males, and one for Females, where for the former a 1 is indicative of the Male category, and a 1 on the latter is indicative of the Female category. However, using that FSGD file and running a DOSS contrast as [0 1 0 0 0], we get the error: matrix is ill-condition or badly scaled, condno=2.01889e+07. We believe this may be due to the fact that Male and Female categories are autocorrelated and Freesurfer likes variables to be de-meaned. Running a FSGD file with only Age and our variable of interest via a DOSS contrast of [0 1 0] works without any errors. We thus created an FSGD file where we have Sex as our third variable (in addition to our continuous variable of interest and one demeaned continuous covariate), coding 1s for Males and 0s for Females, and we used a DOSS contrast of [0 1 0 0]. This provided us with a map that makes sense with our expectations. We would like to verify if this is doing what we believe it is doing; that is, looking at the relationship of our continuous variable or interest after accounting for age and sex. Any thoughts would be greatly appreciated. Thank you so much. Best, Fred

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sub-cortical analysis
by John Anderson 05 Sep '17

05 Sep '17

Hi Dr Greve, I am using pet surfer to analyze suv images. I followed all the steps in wiki, I used the option mgx then I fed the images mgx.{ctxgm,subctxgm,gm} into surface based analysis for left and right hemispheres. I want to inquire about the sub cortical analysis. 1. I assume the analysis for sub cortical gray matter (i.e. using the images subctxgm) is volumetric. Is this correct? 2. Are the following steps correct for sub cortical gray matter analysis mri_vol2vol --mov subctxgm.nii.gz --reg reg.dat --tal --talres 2 --talxfm talairach.xfm --nearest --no-save-reg --o subctxgm.tal2mm.nii.gz mri_mask subctxgm.tal2mm.nii.gz $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz subctxgm.tal2mm_subc.nii.gz & Concatenate all subjects together using mri_concat smooth using mri_fwhm (what is the recommended smoothing for suv)? Then Group analysis: mri_glmfit --y all.suvr.tal2mm.subc.sm10.nii --fsgd fsgd.dat --C contrast.mtx --glmdir dir mri_glmfit-sim --glmdir dir --grf 1.3 pos --cwpvalthresh 0.0166 for "mri_glmfit-sim" in subcortical structure is the flag grf correct or cache? Thanks in advance! John

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individual mri_segstats waveforms for vertices or face in label
by Mcnorgan, Christopher 05 Sep '17

05 Sep '17

Though one workaround might be to subdivide a label many, many times using mris_divide_parcellation, I was wondering if it is possible to obtain a per-vertex (or even per-face) fMRI waveform for a label. In other words, rather than compute the average waveform across all vertices, as with mri_segstats --label subject semi /path/to/label --avgwf avgwave.txt, which yields a single value that averages across, say, 5000 vertices, I would like to obtain each of the 5000 waveforms averaged over. I assume this would be more comparable to the scale of analysis used by those looking at voxel populations (e.g., as in MVPA). Thanks, Chris /********************************************** * Chris McNorgan * Assistant Professor * Department of Psychology * University at Buffalo, * The State University of New York * http://ccnlab.buffalo.edu/ * Office: 716.645.0236 * Lab: 716.645.0222 **********************************************/

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Combining Echo Frames Error
by Maksimovskiy, Arkadiy 05 Sep '17

05 Sep '17

Dear Freesurfer experts, Here are the commands I entered, and errors I received: recon-all -subjid Test01 -i /Testing/T1_MEMPRAGE_4/IM-0002-0206.dcm -autorecon1 #@# MotionCor Thu Aug 31 09:00:15 EDT 2017 Found 1 runs /Users/amaksimovskiy/Desktop/Testing/Test01/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /Users/amaksimovskiy/Desktop/Testing/Test01/mri/orig/001.mgz has 4 frames If this is a multi-frame MEMPRAGE image, use mri_concat --rms to combine echo frames. Could you please advice on how I can run the mri_concat --rms to combine echo frames? Also, would this have to be done before the autorecon1, and then reference the output (dicom or mgz?) into the recon-all command? Thank you for your help and information. - Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

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How to estimate the Intracranial area?
by Zhiliang Long 05 Sep '17

05 Sep '17

Dear FS experts: I'am writting to ask for help about intracranial area. I can find the information of intracranial volume in aseg.stats file. But i did not find the information of intracranial area or is there any way to estimate the intracranial area ? Looking forward to any suggestions. best Zhiliang Long

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Occipital Cortex Segmentation
by Torrado Carvajal, Angel 05 Sep '17

05 Sep '17

Hello, I need to get the segmentation of the occipital cortex. I am attempting to generate the corresponding ROI, using the mri_annotation2label command and then running mris_anatomical_stats to merge the labels and get the actual volume. I am calling mri_annotation2label as follows: mri_annotation2label --subject <ID> --hemi lh --lobesStrict lobefile --outdir 'TEMP' However, I have a couple of questions: 1. Is there any way to generate both lh and rh together? Or should I generate separate volumes and then merge them? 2. What is the structure of the lobefile? I cannot find any example on the wiki. Thank you very much for your help! -- Angel Torrado-Carvajal Postdoctoral Research Fellow Pain Neuroimaging Laboratory MGH/HST Athinoula A. Martinos Center for Biomedical Imaging Building 149, Room 1101, 13th Street, Charlestown, MA 02129 USA atorradocarvajal(a)mgh.harvard.edu | www.nmr.mgh.harvard.edu<http://www.nmr.mgh.harvard.edu> | @MGHMartinos

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Freesurfer Preliminary Questions
by Ledesma, Jason 05 Sep '17

05 Sep '17

To whom it may concern, I am to attend the upcoming Freesurfer course session in Boston, and I would like to ask a few preliminary questions. I am currently attempting to run Freesurfer 5.3 on a windows unit via the Oracle VM VirtualBox Manager. I have tried to follow the instructions of the tutorial thus far, but am having trouble properly downloading the tutorial data into Freesurfer (the data I am attempting to acquire can be found at http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeview) I have tried setting up a shared folder and placing the data in a "Machine Folder", but I still cannot interact with the data. Do you know why this may be? I see that a license key must first be obtained in some instances; perhaps this is the reason there are issues. Also, what is the best way to download the most recent version of Freesurfer on windows? Thank you. Sincerely, Jason Ledesma Staff Research Associate Phone: 1(424)571-7755 E-mail: jason.ledesma(a)labiomed.org<mailto:jason.ledesma@labiomed.org> ________________________________ LA BioMed Warning: This email (and any attachments) is intended for the use of the person to which it is addressed. It may contain information that is privileged and confidential. As the recipient, you are obligated to maintain it in a safe, secure and confidential manner. Unauthorized disclosure or failure to maintain confidentiality may subject you to governmental penalties. Should you not be the intended recipient, please notify us by return email, and delete this message from your computer at once. ________________________________

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Freesurfer August 2017