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30133 discussions

Multiple --meas files in mri_glmfit
by Garikoitz Lerma-Usabiaga 19 Jan '17

19 Jan '17

Hi list, is it possible to have multiple --meas files in mri_glmfit? For example, for a group of 40 subjects, to check in every vertex if there is a relation between CT and the t of a fMRI contrast. Thanks! Gari

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Error running mri_info on OS X (but not Linux)
by Valerie Beck 19 Jan '17

19 Jan '17

Hi, When I run mri_info on my mac (OS 10.11.6) using Freesurfer 5.3, I keep getting this error: WARNING: file /Volumes/skol/VT_MR_2_UD/TVUD1_010/study/cmrr_retinotopy_389_13/IM-0010-0001.dcm does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header But when I run mri_info on my linux machine (Ubuntu 16.04) using Freesurfer 5.3, it runs without error and can read the header info just fine. I looked on the freesurfer wiki and didn’t see any known issues related to this. Thoughts? ~Valerie Valerie M. Beck, Ph.D. Postdoctoral Researcher Department of Psychological and Brain Sciences University of Delaware 108 Wolf Hall Newark, DE (302) 455-8465 vbeck(a)psych.udel.edu<mailto:vbeck@psych.udel.edu>

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mri_mcsim OSX last version
by Garikoitz Lerma-Usabiaga 19 Jan '17

19 Jan '17

Hi list, mri_mcsim on FS5.3 is giving a strange error in osx 10.11, in the wiki a newer Linux version is available and indicates to ask for other versions. Is it possible to have the last osx version? thanks! Gari

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Registration Checking Problems
by Anderson Napolitano 19 Jan '17

19 Jan '17

Good Morning Experts, I am having trouble checking the registration per step 2 of the pet surfer tutorial: http://freesurfer.net/fswiki/PetSurfer. The line: mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta worked just fine but when checking the registration using the line: tkregisterfv --mov template.nii.gz --reg template.reg.lta --surfs I get the following output: set: Variable name must begin with a letter Any advice as to how to resolve this issue will be greatly appreciated. Thanks, Anderson Napolitano?

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mris_make_surfaces error with bbr-init-header
by Sneha Pandya 19 Jan '17

19 Jan '17

Hi all, I have successfully ran recon-all on my subjects with multiple T1s. We want to use flair to refine pial surfaces as for all the subjects pial surfaces are messy and will demand lots of control point edits. After successfully running entire recon-all stream I am running following command to incorporate flair: recon-all -autorecon3 \ -s SUBJ \ -bbr-init-header \ -FLAIRpial \ -bigventricles \ -openmp 12 \ -qcache When I run above command recon-all exits while implementing mris_make_surfaces with an error "Cannot allocate memory" Can someone guide what is happening? Is it that there are large topological error or bbr-init-header flag will only run if I run recon-all from autorecon1 to autorecon3 stage? Thanks, Sneha

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Re: [Freesurfer] pial surface regeneration NOT WORKING
by Bruce Fischl 19 Jan '17

19 Jan '17

Hmmm, not sure what's going on. Can you try this: cd /mnt/Local_Data/Reliability/Matt/5514syxa_110502_3Tnu_HFBd_wmseg/scripts setenv DIAG 0x04048 mris_sphere -w 0 -seed 1234 ../surf/lh.inflated ../surf/lh.sphere and send us the output? On Thu, 19 Jan 2017, Sanjana Shellikeri wrote: > > Hi Freesurfer Developers, > > > We are attempting to regenerate the pial surfaces from an edited > brainmask.mgz. We deleted dura voxels (precentral and postcentral gyri both > hemispheres) on the original brainmask.mgz on Freeview. The command we ran > is: > > > recon-all -autorecon-pial -subjid [subjectID] > > > There was no error output, however, the process hangs indefinitely (>36 > hours) after 'randomSeed 1234' and the pial surfaces have not been > regenerated. > > > Please see the attached text file which contains the terminal output of the > command. > > > We are using xUbuntu 12.04 and freesurfer-Linux-centos4-stable-pub-v5.3.0. > > > > Regards, > > Sanjana Shellikeri, PhD Student > > Department of Speech-Language Pathology > Faculty of Medicine, University of Toronto > 160-500 University Ave. > Toronto, ON M5G 1V7 > sanjana.shellikeri(a)mail.utoronto.ca > >

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WM lobes and Corpus Callosum
by Bharadwaj, Pradyumna - (prad) 19 Jan '17

19 Jan '17

Hi, I've been trying to create WM lobes using the following steps: 1) mri_annotation2label --lobesStrict 2) Outputting the labels from step 1, & creating a simpler annotation without limbic and insular lobes 3) Labeling the WM using mri_aparc2aseg (mri_aparc2aseg --s MySub --annot Step2AnnotationFile --labelwm --hypo-as-wm --wmpar-dmax 20 --rip-unknown However, as the corpus callosum is not labelled as wm, it is not included in any WM lobe. Is there any workaround to assigning the corpus callosum to the different WM lobes or do I have to manually edit aseg.mgz to change the corpus callosum's value to match that of WM ? Thanks, -Prad

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License error when open Tkmedit
by Hao wen 19 Jan '17

19 Jan '17

Hello, FS experts: I installed FS 5.3 and the tkmedit version is stable5, but when I open tkmedit, it always give me the error: ERROR: FreeSurfer license file /Applications/freesurfer/.license not found. But FS 5.3 works fine with the license file license.txt, so I just copy the content of license.txt to .license in the dir of $FREESURFER_HOME, and it still gives me this error,, here is the command ls -la to display all the files:[cid:d53d9bb8-296c-465b-bd70-3712bc44e337] My freesurfer works fine with Freeview or tksurfer, just not work with tkmedit, I even change the .license's right with : chmod +x $FREESURFER_HOME/.license Still does not work, Any advice?? Thanks Hao

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Attrition in longitudinal analysis
by Greenberg, Jonathan 19 Jan '17

19 Jan '17

Dear FreeSurfer users I conducted a longitudinal study with 3 timepoints: baseline, 8 weeks and 24 weeks. Between baseline and 8 weeks participants were randomized to one of 3 training programs. I want to assess changes in gray matter volume from baseline to 8 weeks, and baseline to 24 weeks, and also determine how these changes correlate with various behavioral outcome measures. The correlations will be conducted in SPSS, so I need to export values from each time point to enter into the regression matrix. The issue is that about 20 people dropped out after the 8 week assessment. So to just ask the question about changes in brain structure I created two different processing streams, one for all 75 subjects who have pre and 8 week data, and a second one for the 58 individuals who have pre and 24 week data. Therefore, participants who have data for all 3 time points had their pre and 8-week data analyzed in both processing streams. These separate processing streams yield different pre values for these individuals (e.g. the hippocampal volume of participant X at “pre” in the first processing stream is different than the pre hippocampal volume of the same participant in the second processing stream). My question is about the proper way to combine data from these two processing streams so that I have one Excel column for each of the 3 time points to be analyzed in SPSS with all participants included. One approach would be to use the values from the second processing stream (which includes the 24 week time point) for the participants who have all 3 time points, and use the data from the first processing stream only for those who are missing the 24 week time point. But I am not sure whether this is acceptable given the discrepancy in values between the two processing streams. So, is there better way to combine the data from both streams into these 3 time-point columns? Thank you Jonathan

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Re: [Freesurfer] V6beta: recon-all --noasegfusion does not initialize using longbase aseg.mgz; how to handle aseg edits in longitudinal stream
by Antonin Skoch 19 Jan '17

19 Jan '17

Dear Martin, one more thing: When the error is large and present in both timepoints (as is my case), I think that necessity of editing the same error in both timepoints can easily lead to error (maybe even demonstrated as false positive effect) caused by non-systematic editing. When editing comprises many voxels one cannot realistically assure the perfect consistence in editing. Editing only once (in base) and initialize mri_ca_label in long from base can avoid this problem. So I think the initialization of mri_ca_label from base is not a bad option for such cases. What do you think? Antonin Hi Antonin, the -noasegfusion is not really supported and a left over from initial testing when we first developed the stream. I will take a look at it and probably remove the flag (or implement it in a way that it really initializes with the aseg from the base, although I think this is not desirable, unless one really assumes there is no/ or very little change between time points. About aseg edits in longitudinal processing, please look at our edit wiki page: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits#aseg.mgz <https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits#aseg.mgz> “ ASEG edits can be done in cross, base and long. Recommendation: Edit in long only if you want to correct the volume of important structures. Edit in base if surfaces need to be changed due to incorrect labeling of aseg. Not necessary to edit in cross. The segmentation in the long runs is initialized with a fused aseg (a weighted average of the cross sectional asegs). Thus any edits done to the cross sectionals are incorporated indirectly into the long stream. But since the fused aseg is used only for the initialization, it can happen that manual edits from the cross get removed again. Therefore, to correct the volume, just edit the long." So for your ventricle correction, you could either clean up the cross data and hope it caries over to the long (it should), or directly edit the long aseg. Best, Martin > On 16 Jan 2017, at 23:23, Antonin Skoch <a...(a)ikem.cz> wrote: > > Dear experts, > > I am testing the longitudinal stream with V6beta version. > > The recon-all -help says for -noasegfusion: > > Do not create 'fused' aseg from the longbase timepoints, which would normally > be used to initialize the ca_labeling. Instead, initialize using the longbase > aseg.mgz. > > As I looked to recon-all code it seems that in case of -noasegfusion there is > no use of -r and -ri parameters and therefore no "initialization". Could you > please comment on? > > My second query is regarding manual edits: > > In one subject the manual editing of aseg was necessary due to ventricle > mislabeling. I edited the aseg.presurf in base template and subsequently run > longitudinal stream via > > recon-all -long tpID templateID -noasegfusion -all > > From the last sentence of -noasegfusion help I (wrongly) expected that my > aseg.presurf edits in base template would be incorporated for -long recon. > However, this was not the case, the edits have not been incorporated at all. > Looking at the recon-all code the aseg.presurf from base is never used for > -long. > > I thought that I could incorporate manual edits from base by manual copying > of aseg.presurf from base to long directory. As I looked for the way how the > manual aseg edits are handled in recon-all, they are identified by using the > difference between the files aseg.auto and aseg.manedit which contains manual > edits. Therefore I think that the copying from base is not an option, I > expect that this would replace segmentations not only in manual edit regions, > but in all regions where the aseg.auto of base and aseg.auto of -long differs > (they do not have the same input) which is undesirable. So I think I do not > have any other option than to edit aseg.presurf in -long again. > > Could you please comment on how to optimally handle such situations? > > Regards, > > Antonin Skoch > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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