Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

mkbrainmask-sess and inorm-sess
by Ji Won Bang 04 Mar '16

04 Mar '16

Dear. Freesurfer experts. Hi. How are you? It might be very naive question. When using version 4.5.0 I used the command: mkbrainmask-sess -s $SUBJECT -funcstem fmc -df sessdirfile -fsd bold_retino However under the version 5.3.0, mkbrainmask-sess does not have -funcstem. May I use -maskstem instead of -funcstem? If so, after that, I tried: inorm-sess -s $SUBJECT -motioncor -funcstem fmc -df sessdirfile -fsd bold_retino However, it complains that: ERROR: cannot find /home/jbang/Projects/replay/epi/replay06/bold_retino/masks/brain You may need to run preproc-sess or mkbrainmask-sess to create a brain mask Could you please help? Thank you very much. Best, Ji Won

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Doubts with Longitudinal Analysis Repeated Measures ANOVA
by Universidad de Deusto 04 Mar '16

04 Mar '16

Dear FS Experts, I'm interested in performing Repeated Measures ANOVA 2x2. I have 2 groups and two times (pre and post treatment). I have checked the tutorial for repeated measures anova and previous emails: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg45703.HTML http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg45650.HTML However, it is not clear to me, which steps I have to follow to create the matrix and obtain the results for groupxtime effect. I would be very grateful if someone could help me with this analysis, Thank you in advance, Best Regards

2 1

minimum files to process longitudinal freesurfer
by Ahearn, T 04 Mar '16

04 Mar '16

Hello, I need to process a good few thousand T1 images on a machine that I can't store all the data on. I'd like to transfer as few files as possible to the processing machine so that I can perform longitudinal processing. I have successfully longitudinally processed some patients with a sub set of their data but others seem to hang (the template looks ok) during mri_ca_label. Is there a list of the minimum files that I'd need to perform longitudinal processing? The files I've had some success with are below: /mri/orig/001.mgz /mri/norm.mgz /mri/wm.mgz /mri/aseg.auto_noCCseg.mgz /mri/rawavg.mgz /mri/orig.mgz /mri/brainmask.mgz /mri/aseg.mgz Thanks Trev Dr. Trevor Ahearn Principal Physicist (MRI) NHS Grampian The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683.

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Permission denied error with mri_surfcluster command
by Jennifer Legault 04 Mar '16

04 Mar '16

Dear experts, I am trying to use the cluster thresholding command for my freesurfer LME outputs as referred to here <https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels>. Any feedback or comments would be greatly appreciated. I am aware that there have been permission denied errors when using mri_surfcluster and that applying this patch <ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/mni152reg> should solve the problem (which I tried), however I am still either receiving errors stating the permission is denied. This is the command I am trying to run: mri_surfcluster --subject fsaverage --hemi rh --in rh_time_spval.mgh --cwpvalthresh 0.05 --fdr .05 --sign pos --o rh_time_cluster --sum rh_time_cluster_sum Here is the error log: mri_surfcluster --subject fsaverage --hemi rh --in rh_time_spval.mgh --cwpvalthresh 0.05 --fdr .05 --sign pos --o rh_time_cluster --sum rh_time_cluster_sum thsign = pos, id = 1 version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $ hemi = rh srcid = rh_time_spval.mgh srcsubjid = fsaverage srcsurf = white srcframe = 0 thsign = pos thmin = -1 thmax = -1 fdr = 0.05 minarea = 0 xfmfile = talairach.xfm nth = -1 outid = rh_time_cluster paint sumfile = rh_time_cluster_sum subjectsdir = /gpfs/home/jtl190/work/structurals FixMNI = 1 ------------- XFM matrix (RAS2RAS) --------------- /gpfs/home/jtl190/work/structurals/fsaverage/mri/transforms/talairach.xfm 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; ---------------------------------------------------- Reading source surface /gpfs/home/jtl190/work/structurals/fsaverage/surf/rh.white Done reading source surface Computing metric properties Loading source values number of voxels in search space = 163842 Done loading source values (nvtxs = 163842) overall max = 1 at vertex 27 overall min = 1.52021e-05 at vertex 125620 surface nvertices 163842 surface area 65020.929688 surface area 65020.765625 Setting voxel-wise threshold with FDR = 0.050000 Assuming input map is -log10(p) MRISfdr2vwth(): np = 163842, nv = 163842, fdr = 0.05, vwth=1.04576 FDR Voxel-wise threshold is 1.04576 Adjusting threshold for 1-tailed test. If the input is not a -log10(p) volume, re-run with --no-adjust. Searching for Clusters ... thmin=1.045757 (0.744727), thmax=-1.000000 (-1), thsignid=1, minarea=0.000000 Found 9803 clusters Max cluster size 5993.586426 INFO: fixing MNI talairach coordinates Saving thresholded output to rh_time_cluster Can't create file /gpfs/home/jtl190/work/structurals/fsaverage/surf/rh.rh_time_cluster.w Permission denied Thank you for taking the time to read this email. Sincerely, Jennifer Legault -- Jennifer Legault Ph.D candidate, Neuroscience Brain, Language, and Computation Lab The Pennsylvania State University

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Problem with mriconvert
by Óscar Soto Angona 04 Mar '16

04 Mar '16

Hello, We are medicine students who are using freesurfer for research. We had been using freesurfer in Ubuntu 12.02 without encountering any trouble; recently we updated to 14.04. Now, when we attempt to convert a mgz file to nii using mriconvert, we have an error regarding failure to write the files .nii The command we are using is as follows: mri_convert ../estructural/Freesurfer_segmentacion_cortical_resultado/C2090_cortical_seg.mgz ../estructural/Freesurfer_segmentacion_cortical_resultado/C2090_ cortical_seg.nii The error message we find is this one: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/psa/datos_MRI_cerebral/estructural/Freesurfer_seg_cortical_resultado/C2090_cortical_seg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -4.74975e-08, 0) j_ras = (0, 0, -1) k_ras = (1.21072e-08, 1, 0) writing to ../estructural/Freesurfer_segmentacion_cortical_resultado/C2090.nii... niiWrite(): error opening file ../estructural/Freesurfer_segmentacion_cortical_resultado/C2090.nii ERROR: failure writing ../estructural/Freesurfer_segmentacion_cortical_resultado/C2090.nii We really could use your help, since we can't find any solution in the Internet. Thanks in advance for your attention. Regards, Óscar and Alba

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GLM cluster extending into unparcellated medial surface
by Bronwyn Overs 03 Mar '16

03 Mar '16

Hi Freesurfer mailing list, I have just run a longitudinal 2 stage model using spc (fwhm 10), followed by monte-carlo correction (1.3 abs, cwpvalthresh .05). One of the resulting significant clusters extends into medial regions of the brain that are unparcellated (see attached image). Do you know why this would be happening and what it means? I am using freesufer v5.3. -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe>

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The name of regions of annotation file issue viewing by tksurfer
by Faeze Vedaei 03 Mar '16

03 Mar '16

Hi Freesurfer experts, I have created an annotation file by several label files using mris_label2annot command in Freesurfer. The problem is that when I open this annot file in tksurfer and click on colored regions which corresponded to specific labels I had chosen them, I do not have their name on the vertex information part at the bottom of tksurfer GUI. It shows very different names for these regions. May you explains me what is the problem I could not see the exact region's name as I have them for label files? Thanks, Faezeh Vedaei

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Re: [Freesurfer] conflicting Monte Carlo simulation results...
by Karl Liu 03 Mar '16

03 Mar '16

Dear Doug, Thank you for your clarification. It sounds the right way for correction is:mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4 neg \ --cwp 0.05\ --2spaces One last question: Is the resulting "cache.th40.neg.sig.cluster.summary" the right file to look for post-correction cluster information? The (old) manual said results should be stored in a files starting with "mc-z", but the "cache....summary" file is the only summary file FS produces after running the script above... thank you. Karl ******************************************************** In the first command you only used 5 samples in your simulation. If you read the "Notes" section below the command, you'll see that this should be something like 5000. Only 5 was used because it would take very long to run. In general, you don't need to run the simulation because it has already been run and the data tabulated (this is what is accessed in the 2nd command line).On 03/02/2016 10:03 PM, Karl Liu wrote: > > Dear Freesurfer experts: > > > I ran into a confusing problem when applying Monte Carlo simulation to > control for multiple comparisons. I am using the buckner data from > tutorial dataset. > > > I first tried the simulation based on Freesurfer;s 2012 manual: > > (http://www.freesurfer.net/pub/docs/tarballs_for_courses/FreeSurferTutorial-…) > > > mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --sim mc-z 5 4 > mc-z.negative \ --sim-sign neg --cwpvalthresh 0.05\ --overwrite > > > This produced a "mc-z.negative.sig.cluster.summary". In this text, no > clusters survived correction. > > > Later on, I applied on a slightly different script, based on > Freesurfer tutorial > > (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#Clusterwi…) > > > mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4 neg \ > --cwp 0.05\ --2spaces > > > It produced a "cache.th40.neg.sig.cluster.summary" this time. But > according to this result, 22 clusters survived. > > > Now I am quite confused, because both corrections have the same > voxel-wise (p=0.001) and cluster-wise (p=0.05) threshold. Where the > drastic discrepancies come from and which result is more reliable? > > > Many thinks in advance. > > Best, > > Karl > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in erro

2 1

error in mc-sess
by Ji Won Bang 03 Mar '16

03 Mar '16

Dear. freesurfer experts. Hi. I'm using freesurfer version 5.3.0. I tried mc-sess onto runs that have different number of slices. However, due to this different number of slices in different runs, mc-sess gives an error. I expected that running mc-sess in freesurfer version 5.3.0 would handle this issue. If you can share your idea to fix this problem, that would be a great help. Thank you! Best, Ji Won

2 5

AAL atlas question
by pfotiad＠nmr.mgh.harvard.edu 03 Mar '16

03 Mar '16

Hi FS community, I have recon-ed a set of subjects and I was interested in also obtaining structural info (cortical thickness, gray matter volume, surface area etc.) based on a different atlas than the ones FS is using, and in particular the AAL atlas. I was wondering whether my approach would be the correct one or whether there is another (better and more accurate) approach: 1) Convert the AAL atlas into a surface (with mri_vol2surf) from the MNI space into the native subjects' space, 2) Use mris_anatomical_stats to calculate the structural stats Sorry for the potentially trivial question, and thank you for your time! Best, Panos

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