Freesurfer March 2016

freesurfer@nmr.mgh.harvard.edu

133 participants
229 discussions

ID not identified on surface file
by João V. Dornas 17 Mar '16

17 Mar '16

Dear Friends, I need to 3D render the AAL parcellation volume, with labels (in annotation file) for each ROI. My AAL volume is on MNI152 standard space, with 2mm 91x109x91, as well my results volumes. I used the following command to generate my surface files from my AAL volume. mri_vol2surf --mov aal2std.nii.gz --reg cvs_avg35_inMNI152/mri/transforms/reg.mni152.2mm.dat --projdist-max 0 1 0.1 --interp nearest --hemi lh --out lh.aal2std-1mm_surf.mgz —reshape mri_vol2surf --mov aal2std.nii.gz --reg cvs_avg35_inMNI152/mri/transforms/reg.mni152.2mm.dat --projdist-max 0 1 0.1 --interp nearest --hemi rh --out rh.aal2std-1mm_surf.mgz --reshape Then I tried to create my labels using the following command: mri_cor2label --i lh.aal2std-1mm_surf.mgz --surf cvs_avg35_inMNI152 lh --id 75 --l lh.Pallidum_L I run this command for each one of the 90 ROIs on AAL volume. My problem is that when I execute the last command specifically for Pallidum, both Left and Right (IDs 75 and 76), I found this error: $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $ Loading mri lh.aal2std-1mm_surf.mgz Loading cvs_avg35_inMNI152/surf/lh.white Scanning the volume Found 0 label voxels ERROR: found no voxels matching id 75 It seems that I loose some voxels when I convert from volume voxels to surface vertexes. Do you know what could be happening? I appreciate any help you could give to us. Thanks very much, best regards, -- João V. Dornas Phd student in Neuroscience Cognitive Biology Group, Institute of Biology Otto von Guericke University, Magdeburg Germany

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FreeSurfer 6.0
by Elisabeth Paul 17 Mar '16

17 Mar '16

Dear ladies and gentlemen, for a research project I need to measure the volume of the different hippocampus subregions. I want to use FreeSurfer 6.0 for that but I can only find FreeSurfer 5.3 online. Is FreeSurfer 6.0 not yet released and if so, when will it be released? If it is already released, could you tell me where to find it? Thank you very much in advance. Kind regards, Elisabeth Paul

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gnumeric file
by Caroline Beelen 17 Mar '16

17 Mar '16

Hi FS team, Sorry for these rather basic questions... I'm not sure whether the gnumeric file is an ascii file (see mails below). Attached you'll find the file. It seems the case when you open it in the terminal screen that the nr's look fine (with command cat). However as soon as you type the command gnumeric and so on, it creates a wrong table from the start (see file attached). Can I somehow change this? I have an additional question: I was looking at the Qdec info (tutorial) and I am not totally sure how to create the table.dat file... Where to get the volume measures from, if you'd like to include those? The statistical folder (where the tables are from)? Thank you for responding in advance. Kind regards, Caroline -----Oorspronkelijk bericht----- Van: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Namens Douglas N Greve Verzonden: dinsdag 8 maart 2016 0:24 Aan: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Onderwerp: Re: [Freesurfer] mean thickness the table file lh.aparc.thickness.table should be an ascii file. when you look at it with cat/more/less, what do you see? Can you send that table file? On 03/07/2016 04:33 AM, Caroline Beelen wrote: > Hi Bruce, > > I'm a beginner in FS, so I just followed tutorial instructions for generating the files carefully... > I generated it by typing in for instance (after recon-all process was > done): aparcstats2table --hemi lh --meas thickness --subjects A01_T1 > A02_T1 etc... A10_T1 --tablefile lh.aparc.thickness.table followed by > the command: gnumeric lh.aparc.thickness.table > > It's a linux pc with Ubuntu 12.04 LTS (processor intel core i7-3770 > CPU @ 3.4GHz x 8) > > Attached the log file (A09). > > Thank you very much! > > Greetings, Caroline

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Re: [Freesurfer] Reading values from overlays with PETcoreg
by Elijah Mak 17 Mar '16

17 Mar '16

Dear Doug, Is it possible to use BP SUVR PET that have been registered to T1 for this gtmseg workflow? You mentioned that the mean TAC should be used as the input. 2 quick questions: What's mean TAC and why? Thanks. Best Wishes, Elijah

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WM edit, remove GM bright rim
by Min Liu 16 Mar '16

16 Mar '16

Dear Freesufer users, We have some T1 images having a rim of bright signal in the GM at some spots like the one showing in the attached Figure 1. The WM surface goes out to include this bright signal and the cortex ends up artificially thin. We followed the standard WM edit procedure, which is to erase the bright signal in wm.mgz. As shown in Figure 2, the bright rim is replaced with intensity 1 (red). However, that doesn't improve the situation. Does anyone know a way to prevent the surface from going out? Thanks, -- Min

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Hippocampal subfield segmentation with T1&T2
by Zhuang, Xiaowei 16 Mar '16

16 Mar '16

Dear Freesurfer expert, I am using Freesurfer V6.0 beta version to run the hippocampal subfield segmentation with 2 inputs, a standard T1 and a high resolution T2. Below are the details about the 2 images. T1: resolution: 0.8*0.8*0.8 mm, orientation: Sagittal(S>T4.1>C-0.8) T2: resolution: 0.4*0.4*1.5 mm, orientation: oblique coronal(C>T-14.5>S1.5). The instruction says in order to use both of them for hippocampal segmentation, T2 should be in the same orientation as T1. Therefore, the two images cannot be used directly. Is it possible for me to do some reorient preprocess on the T2 image and then run through the segmentation? Or is it possible to coregister the T1 into T2 space, making them both high resolution and run through the segmentation? Will this affect the Freesurfer pipeline and the final subfields output? Any suggestion will help. Sincerely thanks, Xiaowei. [Cleveland Clinic logo] Xiaowei Zhuang | Research Engineer | Lou Ruvo Center for Brain Health Cleveland Clinic | 888 W Bonneville Ave. | Las Vegas, NV 89106 | (702) 685-6051 =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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surface based analysis using FA maps
by Alshikho, Mohamad J. 16 Mar '16

16 Mar '16

Hi Doug, I would like to run surface based analysis using FA maps. I am not exactly sure that what I am doing is totally right specially step 2 . I used the following commands: 1. I registered the FA maps to T1 using the command: bbregister --s bert --mov dtifit_FA.nii --bold --init-fsl --reg reg.dat 2. I concatenated the subject's FA maps using the command : mris_preproc -target fsaverage -hemi lh -iv .bert1/dtifit_FA.nii reg.dat -iv bert2/dtifit_FA.nii reg.dat .... --projfrac 0.5 --out lh.FA.mgz 3. Then smoothing mri_surf2surf --hemi lh --s fsaverage --fwhm 5 --cortex --sval lh.FA.mgz --tval lh.FA_5mm.mgz 4. Then GLM analysis using mri_glmfit 5. Correction for multiple comparison mri_glmfit-sim Kindly, are these steps correct? I highly appreciate any input on this! Best, Mohamad

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FWHM file not found
by Pedro Rosa 16 Mar '16

16 Mar '16

Dear FreeSurfers, I am running a localgi analysis using mri_glmfit and mri_glmfit-sim, and it seems the last script looked for freesurfer/average/mult-comp-cor/fsaverage/?h/cortex/fwhm40/abs/th13/mc-z.cdf and mc-z.csd, but there are precached data until fmhm30. How should I proceed? Best, Pedro.

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Re: [Freesurfer] group analysis all measures same results
by Douglas N Greve 16 Mar '16

16 Mar '16

this only has to do with the qcache part of recon-all, so you could use version 5.3 recon-all -qcache and it should be fine. However, it is not a good idea to try to publish using the analysis from the version of FS that you used. That was a beta version of version 6 and things will change. On 03/15/2016 01:56 PM, Kaiming Yin wrote: > Dear Douglas, > > Is there anything I can do now to fix this now? I don't want to re-run > all the data again. > > Thanks, > Kaiming > > > On 15 March 2016 at 16:53, Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > OK, this is a bug that I found and fixed in early Nov. Sorry, > that's part of the danger of using a beta version. > > On 03/14/2016 12:22 PM, Kaiming Yin wrote: > > Dear Douglas, > > I re-run the "-qcache" on one data and it took 8 mins to > finish. Still the files are the same, all in 668.6kB size. > > > Kaiming > > On 14 March 2016 at 15:56, Douglas Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > I don't know what happened. I cannot replicate it here. > Can you > re-run the recon-all -s -qcache command and verify that > the files > are still the same? > > > On 3/14/16 11:11 AM, Kaiming Yin wrote: > > Dear Douglas, > > Yes, both of the two pairs of files are the same. i.e. > > mri_diff rh.ad_hv.thick.10.mgh rh.ad_hv.area.10.mgh > > diffcount 0 > > > mri_diff rh.thickness.fwhm10.fsaverage.mgh > rh.area.fwhm10.fsaverage.mgh > > diffcount 0 > > > Does this mean I run the "-qcache" wrongly? I just run > "recon-all > -s XX -qcache" on each subject. > > Thanks, > Kaiming > > > On 14 March 2016 at 14:58, Douglas Greve > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > Check whether rh.ad_hv.thick.10.mgh and > rh.ad_hv.area.10.mgh > are the same, ie, > mri_diff rh.ad_hv.thick.10.mgh rh.ad_hv.area.10.mgh > > If those are the same, then check whether > thickness.fwhm10.fsaverage and > area.fwhm10.fsaverage are the > same in each subject > > > On 3/14/16 10:53 AM, Kaiming Yin wrote: > > Dear Douglas, > > My command lines were, e.g. right thickness > and right white > surface (using the same ad_hv.fsgd and > group_diff.mtx files > in the command lines): > > > ad_hv.fsgd > > GroupDescriptorFile 1 > Title AD_HV_GroupAnalysis > Class AD > Class HV > InputAD_003AD > InputAD_005AD > ... > InputHV_ABHV > InputHV_AEHV > > > group_diff.mtx > > 1 -1 > > > right thickness > > mris_preproc --fsgd ad_hv.fsgd --cache-in > thickness.fwhm10.fsaverage --target fsaverage > --hemi rh > --out rh.ad_hv.thick.10.mgh > > mri_glmfit --y rh.ad_hv.thick.10.mgh --fsgd > ad_hv.fsgd dods > --C group_diff.mtx --surf fsaverage rh > --cortex --glmdir > rh.ad_hv.thick.glmdir > > mri_glmfit-sim --glmdir rh.ad_hv.thick.glmdir > --cache 4 neg > --cwp 0.05 --2spaces > > > right white surface > > mris_preproc --fsgd ad_hv.fsgd --cache-in > area.fwhm10.fsaverage --target fsaverage > --hemi rh --out > rh.ad_hv.area.10.mgh > > mri_glmfit --y rh.ad_hv.area.10.mgh --fsgd > ad_hv.fsgd dods > --C group_diff.mtx --surf fsaverage rh > --cortex --glmdir > rh.ad_hv.area.glmdir > > mri_glmfit-sim --glmdir rh.ad_hv.area.glmdir > --cache 4 neg > --cwp 0.05 --2spaces > > > Their results were all the same. > > Thanks, > Kaiming > > > ---------- Forwarded message ---------- > From: Douglas N Greve > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > To: freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Cc: > Date: Mon, 7 Mar 2016 18:47:11 -0500 > Subject: Re: [Freesurfer] group analysis all > measures same > results > what are your command lines? > > > On 5 March 2016 at 02:01, Kaiming Yin > <yinkaiming6987(a)gmail.com > <mailto:yinkaiming6987@gmail.com> > <mailto:yinkaiming6987@gmail.com > <mailto:yinkaiming6987@gmail.com>>> > > wrote: > > Dear guys, > > I was doing group analysis (command-line) > on two groups > (patients and control, no age or other > information). The > data has been "qcached", and after > following the three > steps as "mris_preproc, mri_glmfit and > mri_glmfit-sim" > shown in the tutorial on the Freesurfer > website, I > obtained the difference on thickness in > both left and > right hemispheres, which seems great. > However, when I > repeated the above steps on other > measures, e.g. area, > area.pial, volume (also replaced the parts of > "thickness" in the command lines), the > results seemed to > be exactly the same again as those in the > thickness > comparison, even the p-value numbers in > the file > "cache.th40.neg.sig.cluster.summary" were > the same. I > was using Freesurfer v6.0-beta, and I > performed the > individual data analysis on a linux > cluster and I > copied/downloaded the whole "qcached" > subject directory > to my linux laptop to perform the group > comparison, both > using the same version of Freesurfer, does > it matter? Or > do you know why it happened like this? > > Thanks, > Kaiming > > > > 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 error > but does not contain patient information, please > contact the > sender and properly > dispose of the e-mail. > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(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/

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LUT in ImageJ
by Kaiming Yin 16 Mar '16

16 Mar '16

Dear guys, Is there a file of "FreeSurferColorLUT.txt" available in the Freesurfer folders, or should I copy/paste the texts to a .txt file directly from the FS website? Also, is there a way to transform this LUT table to enable it to be loaded into ImageJ, or can it work directly well in ImageJ? Thanks, Kaiming

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Freesurfer March 2016