Freesurfer

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30071 discussions

Does recon-all conduct cortical parcellation on the nu.mgz?
by Lee Subin Kristine 22 Feb '17

22 Feb '17

Dear FreeSurfer, Hello, I have been using the preprocessed images (which have already undergone N3 correction) from the Alzheimer's Disease Neuroimaging Initiative database as input for recon-all -all.( version 5.3.1) I have 3 questions: (1) Does recon-all use the nu.mgz during subcortical segmentation and cortical parcellation? (2) If so, then would my image be effectively undergoing N3 "twice", and does this affect the accuracy of the segmentation in any way? (3) A bit of a side question, but does rescaling to isovoxels and performing ACPC aligment before recon-all make the segmentation results more accurate? Thank you in advance. Best regards, Kristine

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Freeview
by N Saf 22 Feb '17

22 Feb '17

Dear Experts, I load the T1 and aseg file in freeveiw and select the lookup table ,and show as isosurface in 3D view for a label .Is it possible to change the color(for example label 13 is blue but I want to show it as yellow!).another question is that if I want to show multiple labels which are not in the range how should I do it ? for example I want to see labels 11 & 13 & 30 but not the lables between ,how can I do it?thanks for your support. Best Regards, Nazanin

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Re: [Freesurfer] -trac-all -prep FS 5.3 Memory Allocation Issue
by Yendiki, Anastasia 21 Feb '17

21 Feb '17

Hi Abby – When you say you have successfully processed a subject on that machine before, what FS version was that with? What has changed since then? The last I remember memory allocation issues, they were years ago in a very old version of OSX that we don’t even distribute binaries for any more, so I don’t think this is the same problem. Best, a.y From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Abigail Waters <awaters2(a)suffolk.edu<mailto:awaters2@suffolk.edu>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Friday, February 10, 2017 at 3:05 PM To: "freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] -trac-all -prep FS 5.3 Memory Allocation Issue Hello - I'm attempting to run the -trac-all -prep command with FS 5.3. I am running into the same memory allocation issues on my Mac that were present in earlier versions of Freesurfer/Tracula. See below: MRIallocSequence (218, 182, 1):could not allocate 158784 bytes for the 44th slice Cannot allocate memory I have attempted the pre-processing with multiple and single subjects. I have successfully processed a single subject on this machine before, and have not updated to the latest Freesurfer since that subject (as all MPRAGE scans were reconstructed is FS 5.3). There is sufficient memory available and the MPRAGE scans were reconstructed correctly. Any thoughts on how to solve the issue would be appreciated. Please let me know if you need any additional information. Thanks! Abby

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contrast matrix for one-way ANOVA with 1 factor, 4 groups
by Gold, Andrea (NIH/NIMH) [F] 21 Feb '17

21 Feb '17

Hi, I am trying to run a cortical thickness analysis comparing four groups – my goal is to conduct an omnibus F-test testing for any group differences. I have 0 covariates/nuisance regressors. This would be equivalent to the “Contrast 4 group.effect.mtx” in this page, for 3 groups: https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V But, instead of 3 groups I have 4 groups. I thought the contrast matrix for 4 groups F-test would be: 1 -1 0 0 0 1 -1 0 0 0 1 -1 But for 3 groups it is: 1 -1 0 1 0 -1 Would you please clarify the correct contrast matrix for this test in Freesurfer mri_glmfit? Thank you! Andrea -- Andrea Gold, Ph.D. Section on Development and Affective Neuroscience National Institute of Mental Health 9000 Rockville Pike MSC 2670 Bldg. 15K Bethesda, MD 20892 Phone: 301-402-6955 Fax: 301-402-2010 Email: andrea.gold(a)nih.gov

2 2

Cerebral (without ventricles) Volume = aseg.stats / SupraTentorialNotVent ?
by Kaiming Yin 21 Feb '17

21 Feb '17

Dear guys, Could I ask which value in the stats/aseg.stats represents the volume of the cerebrum (including the subcortical structures while excluding the ventricles and brain stem)? I'm not sure whether the "SupraTentorialNotVent" can be the value for this measurement, and could it be a bit bigger than the real value due to the partial volume effect? Besides, could I also ask is there a value represent the volume of the cerebellum? Currently I calculate the volume by adding the left/right cerebellar GM/WM values in the detailed list in aseg.stats file. Many thanks, Kaiming

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cannot "git pull" from freeSurfer git repository
by Antonin Skoch 21 Feb '17

21 Feb '17

Dear experts, I am recently not able to pull from freeSurfer git repository. The error message is following: error: The requested URL returned error: 403 Forbidden (curl_result = 22, http_code = 403, sha1 = b3b71d49c42db73a6f1dad0229111dc3f900a1d3) error: Unable to find b3b71d49c42db73a6f1dad0229111dc3f900a1d3 under https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/repo/freesurfer.git Cannot obtain needed object b3b71d49c42db73a6f1dad0229111dc3f900a1d3 error: fetch failed. Git clone to the fresh empty directory exits with similar error. Did you recently forbid access to freeSurfer git repository to external users? Regards, Antonin Skoch

1 0

mri_glmfit-sim
by Shane Schofield 21 Feb '17

21 Feb '17

Hi, I have 3 beginner questions about the use of mri_glmfit-sim 1. Under what type of circumstances should I run mri_glmfit-sim with permutation simulations? 2. The voxel threshold of 0.01 (cache 2) is used a lot. Is this too lenient in cortical thickness comparisons? 3. About the sign of the test (abs, neg, pos): is a one-tailed sign justified if I have an hypothesis? If the uncorrected (mri_glmfit) test shows a significant difference in one direction but not the other, am I justified to use pos/neg (instead of abs) in the mri_glmfit-sim stage and explicitly state that in the manuscript? Thanks. Hope to learn more. Have a good week. Cheers, Shane

2 1

Re: [Freesurfer] Convolving external regressors with HRF
by Reza Rajimehr 21 Feb '17

21 Feb '17

Hi Doug, Since our external regressors are stimulus-related (e.g. mean luminance of stimuli), we need to convolve them with a hemodynamic response function. In mkanalysis-sess, we have used -spmhrf 0 to model conditions. Is there a code or Matlab script for HRF convolution, so that we apply exactly the same spmhrf function for modeling the external regressors? Thanks, Reza No, they are not On 02/17/2017 05:09 PM, Reza Rajimehr wrote: >* During the functional analysis in FS-FAST, are the external regressors *>* convolved with the hemodynamic response function? *>>* Thanks, *>* Reza *>>>* _______________________________________________ *>* Freesurfer mailing list *>* Freesurfer at nmr.mgh.harvard.edu <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> *>* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> * -- Douglas N. Greve, Ph.D. MGH-NMR Centergreve at nmr.mgh.harvard.edu <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2www.nmr.mgh.harvard.edu/facility/… Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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cluster as ROI
by Clara Kühn 21 Feb '17

21 Feb '17

Dear FreeSurfer Experts, I compared 2 groups in QDEC in spc (from pre to post) and found a cluster that survives Monte Carlo correction. Now I would like to extract the data for each participant and each time point from that cluster so that I can plot the change. How could I do this? I tried this so far: aparcstats2table --qdec-long $SUBJECTS DIR/qdec/2016.12.06-40kids-long.qdec.table2-1.dat --hemi rh - -tablefile $SUBJECTS DIR/qdec/2016.12.08-40kids-2stagemodel/rharea-cluster-extracted.txt --parc $SUBJECTS DIR/qdec/2016.12.08-40kids-2stagemodel/rh-area again/rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh But I get this error: ERROR: The stats file /nobackup/etsch2/kids/prepost-61kids/AL3K_1.long.AL3K.base/stats/rh./nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again/rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files Do I have to define my cluster as a ROI and then warp it onto the single time points? How would I do that? Any help is much appreciated! Thank you Clara -- Clara Kühn, Phd Student Max-Planck-Institute for Human Cognitive and Brain Science Department of Neuropsychology Stephanstrasse 1A 04103 Leipzig, Germany Phone: +49 341 - 9940 2271 Fax: +49 341 - 9940 2260 Web: www.cbs.mpg.de E-Mail: ckuehn(a)cbs.mpg.de

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Convolving external regressors with HRF
by Reza Rajimehr 21 Feb '17

21 Feb '17

During the functional analysis in FS-FAST, are the external regressors convolved with the hemodynamic response function? Thanks, Reza

2 1

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