Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30064 discussions

Fixed Effects Analysis on Single Subject's Brain
by Taylor, Johnmark 05 Sep '17

05 Sep '17

Hello, Quick question. If I scanned a single subject across several sessions and want to do a fixed effects analysis on that subject's brain (without registering to MNI or Talairach space), how do I go about doing this? I am trying to us isxconcat-sess and then mri_glmfit, but I am not seeing an option to simply do the analysis in native space instead of registering to a standard brain. Is there a way to do this besides taking the end result of the analysis and doing the reverse registration back to the subject's brain? JohnMark

2 1

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 **********************************************/

2 1

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

2 1

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

3 2

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

2 1

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. ________________________________

3 8

Map of covariance
by stdp82＠virgilio.it 05 Sep '17

05 Sep '17

Hi list,by applying a design e.g. 4GV1 in fsgd I could assess the dependence of group differences taking in account the effect of covariate.Anyway, where I should look if I want assess the the map showing the clusters in which the dependent variable is associated to covariate, tacking in account the group difference? Please could you suggest my the path?Thanks Stefano

2 1

upsampling ?h.curv
by shahin＠nmr.mgh.harvard.edu 05 Sep '17

05 Sep '17

Dear Freesurfers, I want to project a map on up-sampled inflated brain. Up-sampled inflated brain has been generated using mris_mesh_subdivide command (without any problem). But when I apply the same command to ?h.cuv I get an error message that: ERROR: MRISread: file 'surf/rh.curv' has many more faces than vertices! Probably trying to use a scalar data file as a surface! I even tried to regenerate ?h.curv files using mris_make_surfaces as below: mris_make_surfaces -c -white rh.white_upsampled subjid ?h But this command automatically down-sample rh.curv after down-sampling rh.white. Regards

3 4

Interpretting Brain Segmentation Volume to eTIV ratio
by Mehta, Chintan 05 Sep '17

05 Sep '17

Dear FreeSurfer community, I wanted to interpret the BrainSegVol.to.eTIV ratio that is outputted from FreeSurfer version 5.2.0. In my sample of normally developing adolescents of ages 8 to 21, this ratio is between 0.65 and 0.85 for 98% of subjects. However, the value is less than 0.65 for 2% of subjects. Could this reflect actual feature of brain volume to eTIV? Or is this a reflection of poor scans, poor overall FreeSurfer processing, or inaccurate eTIV estimates for these subjects? Subjects with BrainSegVol.to.eTIV ratios less than 0.65 tended to all be females. They had Brain Segmentation volumes falling in normal ranges of females in the full sample. However, their eTIV was on the upper-end among eTIVs of females in the sample. If the eTIVs for these subjects were over-inflated, then it makes sense the ratios are especially low. Thank you. Best, Chintan

2 1

group interaction with one continuous covariate and three nuisance variables (two continuous, one dichotomous)
by Ines Mürner-Lavanchy 05 Sep '17

05 Sep '17

2 1

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