Freesurfer July 2011

freesurfer@nmr.mgh.harvard.edu

129 participants
195 discussions

stats files query
by Rebecca McCourt 20 Jul '11

20 Jul '11

Hi, I see that some stats files are more reliable than others for certain types of data, for instance I read that aseg isn't that reliable for WM/GM. Which files I should use to find cortical thickness (whole-brain and each hemisphere), GM/WM volumes (cortical) and whole brain volume? What's the difference between mris_anatomical_stats and mri_segstats, and which of these should I use to get the data specified above? Thanks in advance for your help, Rebecca M

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Calculate WM, GM and CSF volume
by Fellhauer, Iven 20 Jul '11

20 Jul '11

Dear All, I want to calculate the volume of WM, GM and CSF. First of all I have converted the .mri files to .mgz files. I have checked the ReconAllDevTable page to get the recon-all switches to calculate the volume of GM, WM and CFS. I want to use the following switches to calculate the volume, but I' m not sure if this works/is right: recon-all -autorecon1 - gcareg -canorm -careg -rmneck -skull-lta -calabel -segstatts -subject <subject> Did I miss something? Is there a better/faster way to get/calculate the volumes? The command returns the correct results? Best regards, Iven Fellhauer

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mgz to nii.gz... T1 and ROIs. Is there a way to do (5) from command line?
by r.navarra＠itab.unich.it 20 Jul '11

20 Jul '11

Hi FS expert. I need to port my T1 and a couple of ROIs from mgz to nii.gz. The same for many subjects. The issue's about dimensions. When I use fslview, it respond me that "All overlays must have same dimensions as the base image!". Indeed T1's 256x256x256 with voxel sizee 1mm3, ROIs are differents dimensions and 0.5mm3 voxel size. To work now I use this pipeline: ( command line :) ) 1) mri_convert ---> nii 2) gzip ---> nii.gz 3) fslmaths t1 -sub t1 t1_zero 4) mricron t1_zero -l 0 -h 100 -o roi1.nii.gz ( GUI only :( ) 5) (from mricron) save as nifti roi1_ok.nii.gz Is there a way to do (5) from command line? Thanx Riccardo

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finding closest vertex in matlab
by Corey Keller 19 Jul '11

19 Jul '11

Hi Freesurfers, I have talairach coordinates of electrodes sitting on the brain. I am hoping to use the Desikan-Killiany parcellation scheme to determine which cortical region each electrode lies closest to in standard space. I am using read_annotation in matlab to read the lh.aparc.annot file and find the vertices associated with each label. I am wondering how to determine which label each electrode lies closest to? Is there a TAL or RAS to vertex function in matlab? Thanks. Best, Corey

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Re: [Freesurfer] Defining an mrs voxel in the anatomical dataset for partial volume correction
by Douglas N Greve 19 Jul '11

19 Jul '11

Sorry, I don't know anyone who can help with that. As you note, people do it, so there must be people around who can extract the relevant information out of the header. The information you need are the direction cosines and RAS of the corner of the voxel. You can feed this into mri_volsynth. To register to FS, you'll need to have a whole-brain volume collected during the same session. If you collected the anatomical analyzed in FS at the same time, then you don't need another. If you did not, you can literally use any whole brain acquisition, eg, a single TR of an EPI (less than 10 sec to acquire). You can then register the EPI to the anatomical with bbregister. This gives you a "register.dat". You can then concatenate that with the EPI-MRS registration (I can show you how). After that, you can run mri_compute_volume_fractions passing it the synthesized volume and the register.dat (or identity matrix if same session). Another alternative is to collect an actual MRI volume that spans your MRS volume. You can then substitute that for the synthetic volume. Note that the actual pixel content of this volume is irrelevant -- it's just used to get geometry information out of it. This will be the easiest if you can do it. doug _andreia_(a)sapo.pt wrote: > Hi Doug, > > Do you know who can help me with this? That's exactly what I think > that I need to do... The thing is that, unfortunately, I can't find > anyone who can describe how the creation of an MRI "volume" from the > MRS voxel is done, although this approach is present in many many papers. > > About the second part, how do I register the synthetized MRI "volume" > to the FS anatomical? And how can I get the volumes of only that > "volume"? > > (Hopefully I'll find a way to do the first part...) > > Thanks, > Andreia > > > > > Citando Douglas N Greve <greve(a)nmr.mgh.harvard.edu>: > >> Hi Andreia, I've done this before using information in the spectroscopy >> header, then synthesizing an MRI "volume" with one voxel that covers the >> size of your spectroscopy voxel, then registering that to the FS >> anatomical, then computing the partial volume fractions from the >> anatomical. The hard part is the first step, which I can't really advise >> you on. >> >> doug >> >> _andreia_(a)sapo.pt wrote: >>> Dear list, >>> >>> I am performing single-voxel and multivoxel spectroscopy analysis and >>> I need to do partial volume correction. I found a thread on the list >>> of someone asking if it possible to achieve this using Freesurfer (see >>> below), but there is no answer saying how it is done. My question is >>> how can I define the voxel (for single-voxel) and the chosen voxels >>> (for multivoxel) in the anatomical data set to use the segmentation of >>> only that defined voxel? I'm using a Siemens TrioTim 3T. All >>> acquisitions are in the same session. The anatomical dataset is an >>> average of 2 MPRAGEs which I've already processed using FS, and the >>> spectra files are .rda. The header of the MRS data has info on >>> vectors, but I don't know how to use them. >>> >>> >>> >>> "Re: [Freesurfer] need info for beginner >>> >>> Bruce Fischl >>> Thu, 26 Apr 2007 11:17:01 -0700 >>> >>> Hi Pom, >>> >>> yes, people here are using it for spectroscopy and for partial volume >>> correction (also for voxel placement). >>> >>> cheers, >>> Bruce >>> >>> On Thu, 26 Apr 2007 [EMAIL PROTECTED] wrote: >>> >>> Hi, >>> >>> I am about to install FREE SURFER for my Spectroscopy work. >>> I want to use the software to perform GM/WM segmentation on my >>> single voxel data sets. >>> >>> I am wondering if any one on this mailing list is currently >>> doing this task. I would like to get comments. >>> >>> My study is on a GE 3T scanner. >>> >>> thank you, >>> >>> Pom" >>> >>> >>> >>> Any advice, please? >>> >>> Thank you! >>> >>> Andreia >>> >>> >>> -- >>> >>> Andreia Pereira, MSc student >>> Visual Neuroscience Laboratory >>> IBILI-Faculdade de Medicina >>> Azinhaga de Santa Comba >>> 3000-354 Coimbra Portugal >>> Phone +(351) 239480220 >>> Fax +(351) 239480280 >>> >>> ------------------------------------------------------------------------ >>> >>> >>> _______________________________________________ >>> 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 >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> _______________________________________________ >> 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 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 Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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recon-all taking a really long time
by Jonathan McDaniel 19 Jul '11

19 Jul '11

Hi, I have been running a surface reconstruction for over 19 days now, and it is still in the process of correcting defects. Based on how long it took to do one hemisphere (it is now on the second) it appears it will be done hopefully within 3 days. I have been concurrently running other subjects on the same quadcore machine, using 3 of the 4 processors to perform the recons, and they have been finishing in a normal amount of time. Has anyone else had a brain take this long to run? Should I suspect that something is wrong with the inputted dicom files? Are manual edits necessary to fix some of the defects to speed up the process? Thanks for your answers! Jonathan

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Having Matlab portion run as compiled matlab
by Bill Taylor 19 Jul '11

19 Jul '11

So I peaked in archive and did not get a hit. The situation is that the University of Wisconsin Madison site license prohibits us running Matlab in a cluster unless it is compiled. I am assisting a Neurology lab with having a Condor workflow which this time round will do both Matlab and FSL post processing. To compile the Matlab one needs to compile the entry points. But to run it, we'd have to change how it is called. Anyone have pointers for me? Bill Taylor Center for High Throughput Computing Condor Project Computer Sciences University of Wisconsin, Madison 608-219-4430

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Running autorecon2-wm
by Antonella Kis 19 Jul '11

19 Jul '11

Hi Bruce, Based on your last suggestion, after running the recon-all on my NPI001 subject: recon-all -s NPI001 -i /usr/local/freesurfer/subjects/june2011/_orig_/NPI001.nii.gz -qcache -all and editing the wm, I saved all my edits (using the tool box menu as Save Volume As) under wm_edits_before.mgzm and I checked to make sure the edits are there/saved. Now I need to run autorecon2-wm and autorecon3 and I am not sure if in the subjid I still need to write NPI001 (in this case how Freesurfer knows that my wm edits are in the wm_edits_before) or I need to run the following syntax: recon-all -autorecon2-wm -autorecon3-s NPI001 -i /usr/local/freesurfer/subjects/june2011/_orig_/NPI001/mri/wm_edits_before.mgz ? Thank you very much. Antonella

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which files for thickness and volume stats?
by Rebecca McCourt 18 Jul '11

18 Jul '11

Hi all, I'm wondering which files I should use to find volumetrics data... I need cortical thickness (whole-brain and each hemisphere), GM/WM volumes (cortical) and whole brain volume. I know about asegstats2table but I read that aseg isn't that reliable for WM/GM. What's the difference between mris_anatomical_stats and mri_segstats, and which of these should I use to get the data specified above? Thanks! Rebecca M University of Alberta

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Re: [Freesurfer] Problem registering labels to native space
by John Richey 18 Jul '11

18 Jul '11

Hi Doug, this is indeed an fsfast analysis. I used the fsaverage subject included with the 5.1 distribution. Here is the code that I used to produce the registration matrix for one subject. Note that I did use mri_convert to change the .mgz files into .nii.gz The use of flirt (below) is more of an ad-hoc solution to register each subject's anatomical image to fsaverage. I'm not wedded to this method if there's a better alternative. bet ${SUBJECTS_DIR}/${SUBJECT}/mri/nu.nii.gz \ ${SUBJECTS_DIR}/${SUBJECT}/mri/nu_bet.nii.gz \ -f 0.3 -g 0 flirt -in ${SUBJECTS_DIR}/${SUBJECT}/mri/nu_bet.nii.gz \ -ref ${SUBJECTS_DIR}/fsaverage/mri/brain.nii.gz \ -out ${SUBJECTS_DIR}/${SUBJECT}/mri/nu_bet_reg.nii.gz \ -omat ${SUBJECTS_DIR}/${SUBJECT}/mri/nu_bet_reg.mat \ -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 \ -searchrz -90 90 -dof 12 -interp trilinear cd $SUBJECTS_DIR tkregister2 --targ $SUBJECTS_DIR/${SUBJECT}/mri/nu_bet_reg.nii.gz \ --mov $SUBJECTS_DIR/fsaverage/mri/brain.nii.gz \ --fsl $SUBJECTS_DIR/${SUBJECT}/mri/nu_bet_reg.mat \ --reg $SUBJECTS_DIR/${SUBJECT}/mri/nu_bet_reg.dat \ --noedit -----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Monday, July 18, 2011 3:11 PM To: John Richey Cc: 'Bruce Fischl'; 'freesurfer(a)nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] Problem registering labels to native space How did you create it? What is the actual "fsaverage space"? Is this an FSFAST analysis? doug John Richey wrote: > Hi Doug, the .dat file that I mention below had already been converted into > a fs matrix using tkregister2. > > -----Original Message----- > From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] > Sent: Monday, July 18, 2011 12:38 PM > To: John Richey > Cc: 'Bruce Fischl'; 'freesurfer(a)nmr.mgh.harvard.edu' > Subject: Re: [Freesurfer] Problem registering labels to native space > > You can't use a flirt matrix with mri_label2label. You can convert a > flirt matrix to the proper format with tkregister2 using the --fsl > option (this will allow you to check the reg as well). > > doug > > John Richey wrote: > >> Hi Bruce, >> >> The labels that I have fsaverage space are 3D/volume-based and not >> surface-based labels. >> >> >> -----Original Message----- >> From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] >> Sent: Monday, July 18, 2011 12:00 PM >> To: John Richey >> Cc: 'freesurfer(a)nmr.mgh.harvard.edu' >> Subject: RE: [Freesurfer] Problem registering labels to native space >> >> Hi John >> >> why are you using an affine volume registration for fsaverage? Why >> not use surface registration? >> >> Bruce >> >> >> On Mon, 18 Jul 2011, John Richey wrote: >> >> >> >>> Hi Bruce - thanks for the reply. >>> >>> Here is my command line: >>> >>> mri_label2label --srcsubject fsaverage \ --trgsubject ${SUBJECT} >>> --srclabel $SUBJECTS_DIR/group_analysis/${CONTRAST}/${LABEL} \ >>> --trglabel $SUBJECTS_DIR/${SUBJECT}/label/${CONTRAST}_${LABEL} \ >>> --regmethod volume \ --reg $SUBJECTS_DIR/$SUBJECT/mri/brain_reg.dat >>> >>> Where "brain_reg.dat" is the subject-specific matrix I created >>> through FLIRT. However, as I mentioned, disincluding this matrix >>> does not seem to change the result much. >>> >>> One other problem I encounter... Occasionally when I view the label >>> in native space, the label itself seems to be eroded on a voxel-wise >>> >>> >> basis. >> >> >>> That is, the label essentially appears as a series of non-contiguous >>> dots (which if dialated would become contiguous). >>> >>> >>> >>> >>> >>> >>> -----Original Message----- >>> From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] >>> Sent: Monday, July 18, 2011 11:20 AM >>> To: John Richey >>> Cc: 'freesurfer(a)nmr.mgh.harvard.edu' >>> Subject: Re: [Freesurfer] Problem registering labels to native space >>> >>> Hi John >>> >>> can you email us your label2label cmdline? >>> >>> cheers >>> Bruce >>> >>> >>> On Mon, 18 Jul 2011, John Richey >>> wrote: >>> >>> >>> >>>> Dear freesurfer experts, >>>> >>>> I have a series of labels corresponding to clusters of significant >>>> activation in fsaverage space. >>>> >>>> I want to map these back to native space using mri_label2label, >>>> however when I view the individual (native) labels, the >>>> registration is way off and the labels do not map into plausible space. >>>> >>>> I have tried using talairach space as an intemediary (by omitting >>>> the --reg flag in mri_label2label), as well as using fsl tools >>>> (FLIRT) to create a registration matrix but unfortunately I cannot >>>> seem to get the label into the right space to query my ces maps in >>>> > funcroi-sess. > >>>> Have others encountered this problem? And how might I create a more >>>> robust registration between fsaverage and native space to >>>> facilitate the spatial transformation of my labels? >>>> >>>> Thanks very much in advance, >>>> John >>>> _______________________________________________ >>>> 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 error but does not contain >>> patient information, please contact the sender and properly dispose >>> of the >>> > e-mail. > >>> >>> >>> >> _______________________________________________ >> 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 > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Freesurfer July 2011