Freesurfer September 2014

freesurfer@nmr.mgh.harvard.edu

120 participants
164 discussions

Re: [Freesurfer] Cortical gray matter surface area
by will brown 08 Sep '14

08 Sep '14

Sorry, my mistake. I did mean surface area rather than volume. I am unsure as to how to find the total surface area of the cortical gray matter as ?.aparc.stats file only report WhiteSurfArea. Thanks, Will Message: 17 Date: Wed, 27 Aug 2014 00:48:29 -0400 From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cortical gray matter surface area To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <53FD631D.4070608(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset="iso-8859-1" The volume for each structure is given as the 4th column. If you want total GM volume, look in aseg.stats doug On 8/26/14 8:43 PM, will brown wrote: > Hi all, > > I am a little unclear as to how to find the cortical grey matter > volume in the stats output files. The ?.aparc.stats file shows: > > Measure Cortex, WhiteSurfArea, White Surface Total Area, XXXX, mm^2 > > What about grey? > > Thanks, > Will

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seed-based functional connectivity: mkcontrast-sess
by Robby De Pauw 08 Sep '14

08 Sep '14

Dear FreeSurfer community, I was wondering what my contrast-matrix should look like when doing a first-level analyses since there is no task involved. I tried looking at the -help flag, but I can’t see any options for setting a matrix without entering the numb of conditions. This was the command I tried to use: mkcontrast-sess -rmprestim -analysis restingstate.sm05.lh -contrast restingstate.lh I’m sure I’m missing something here, but I can’t figure out what to do. Thanks for the already given support!! Best regards, Robby Robby De Pauw, dra. Ghent University Department of Physiotherapy and Rehabilitation Sciences 3B3 De Pintelaan 185 B-9000 Ghent Robby.DePauw(a)Ugent.be

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Freesurfer at 7T
by Lucy Hiscox 07 Sep '14

07 Sep '14

Dear Freesurfer experts, I am currently trying to segment a 7T image at 0.8 isotropic resolution. I have an MPRAGE scan and a Gradient echo, and want to coregister the data before processing to correct for inhomogenities, but unsure whether I can use FSL instead of SPM. I am following these instructions: https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon I am new to SP8 and not sure what I would have to do with this information specifically: (i1./i2 .* (i2>20)) .* 100. Also, is it possible to just use the recon-all process or would you recommend going through each step individually outlined above? Is the second option the option for keeping the voxels at 0.8? Furthermore, I read somewhere that you have to use the -cm -aseg command to keep the voxels the same. is this true? Best wishes and many thanks, Lucy -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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about issues with "recon-all"
by Abel Lei 06 Sep '14

06 Sep '14

Hi FreeSurfers, I’m a very beginner to both the Linux OS and the FreeSurfer program. After finally setting up the FreeSurfer, I was trying to do recon-all for my trial subject. But when I ran the “recon-all” command, it returned with a long error message indicating many commands not found. The message is copied and pasted below. I also attached the recon-all.log and recon-all.error in this email, which (probably) contains two failed attempts of the same command. Please let me know if you need any other info from me. I appreciate your help and time greatly! Thank you so much! Chia-Ming (Abel) Lei PhD Student/Graduate Student Researcher Language and Brain Lab (LABlab) & Adult Language Lab Department of Communication Sciences and Disorders School of Health and Rehabilitation Science University of Pittsburgh -----below is the long~ error message------ chiaming-PORTEGE-R835:~> recon-all -all -s mike_dickeySubject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot Actual FREESURFER_HOME /home/chia-ming/Desktop/freesurfer -rw-rw-r-- 1 chia-ming chia-ming 2119 Sep 6 01:34 /home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot/mike_dickey/scripts/recon-all.log Linux chiaming-PORTEGE-R835 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux mri_motion_correct.fsl: Command not found. talairach_avi: Command not found. tkregister2_cmdl: Command not found. nu_correct: Command not found. mri_make_uchar: Command not found. mri_normalize: Command not found. mri_watershed: Command not found. mri_gcut: Command not found. mri_segment: Command not found. mri_label2label: Command not found. mri_em_register: Command not found. mri_ca_normalize: Command not found. mri_ca_register: Command not found. mri_ca_label: Command not found. mri_pretess: Command not found. mri_fill: Command not found. mri_tessellate: Command not found. mri_concatenate_lta: Command not found. mri_normalize_tp2: Command not found. mris_smooth: Command not found. mris_inflate: Command not found. mris_curvature: Command not found. mris_sphere: Command not found. mris_fix_topology: Command not found. mris_topo_fixer: Command not found. mris_ca_label: Command not found. mris_euler_number: Command not found. mris_make_surfaces: Command not found. mris_register: Command not found. mris_volmask: Command not found. mris_anatomical_stats: Command not found. mrisp_paint: Command not found. mris_curvature_stats: Command not found. mris_calc: Command not found. mri_robust_register: Command not found. mri_robust_template: Command not found. mri_and: Command not found. mri_or: Command not found. mri_fuse_segmentations: Command not found. mri_segstats: Command not found. cp: cannot stat 'Desktop/freesurfer/bin/recon-all': No such file or directory #-------------------------------------------- #@# MotionCor Sat Sep 6 01:40:13 EDT 2014 ERROR: no run data found in /home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot/mike_dickey/mri. Make sure to have a volume called 001.mgz in /home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot/mike_dickey/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Linux chiaming-PORTEGE-R835 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s mike_dickey exited with ERRORS at Sat Sep 6 01:40:13 EDT 2014 For more details, see the log file /home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot/mike_dickey/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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LGI Topological Defect
by Tara Miskovich 06 Sep '14

06 Sep '14

Hi all, I am getting an error that seems common for people running LGI where it crashes due to a topological defect. I have run mris_euler_number and everything looks fine. Plus, I went through each slice and made sure the surfaces looked good. Any advice on any other steps I can take? I have already tried rerunning recon-all. Thank you! Tara

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Re: [Freesurfer] tracula: bvec-error
by Robby De Pauw 05 Sep '14

05 Sep '14

Hi Anastasia, I’m using this version of tracula. trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp I’ve attached the log-file you requested. Robby De Pauw, dra. Ghent University Department of Physiotherapy and Rehabilitation Sciences 3B3 De Pintelaan 185 B-9000 Ghent Robby.DePauw(a)Ugent.be

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Nframes greater than 1...
by Gonzalo Rojas Costa 05 Sep '14

05 Sep '14

Hi: I have an mprage image with nframes = 2... how can I convert it to use it in freesurfer ?... Sincerely, Gonzalo Rojas Costa -------------------------------- Gonzalo Rojas Costa Advanced Medical Image Processing Laboratory Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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Re: [Freesurfer] trac-all -prep error field map error
by Eileen Moore 05 Sep '14

05 Sep '14

Hi - I still have not been able to apply the field map correction within tracula. Tracula does not appear to recognize the format of my field maps in either dicom or nifti formats. However, as a work around I first did the field map correction outside tracula (using our wrapper script for epidewarp). Next I used this field map corrected image as the input diffusion image for tracula and set dob0 = 0 in my dmrirc file (so as to skip tracula's field map correction). This appears to be working. Eileen. > > ------------------------------ > > Message: 5 > Date: Wed, 27 Aug 2014 13:51:06 -0700 > From: Eileen Moore <eimoore(a)mail.sdsu.edu> > Subject: Re: [Freesurfer] trac-all -prep error field map error > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <CA++dajQo_2EF= > LvUFCKbs+_061v7dcTFC5T11PN0K4G9d-CuAw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Anastasia, I'm not sure how I can give tracula the phase difference maps, > can you provide an example? > > As a reminder, I've run a wrapper script around epidewarp which takes our > dicom images and converts them into a phase difference map (it is based on > the script that was authored by Doug Greve for the fBIRN consortium). > > In the tutorial dmrirc example I see only the 'set b0mlist' and 'set > b0plist' options, and am unsure where I could give it the phase difference > map. > > I've also tried converting the dicom magnitude and phase maps to nifti > format and inputting these into the dmrirc file but I am still getting an > error. (See attached log file). > > Thanks, > Eileen. > > > > > ------------------------------ > > > > Message: 10 > > Date: Thu, 17 Jul 2014 04:14:16 -0400 (EDT) > > From: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > > Subject: Re: [Freesurfer] trac-all -prep error field map error > > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > > Message-ID: <alpine.LRH.2.03.1407170411110.12767(a)nmr.mgh.harvard.edu> > > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > > > > > Hi Eileen - All image formats that mri_convert (and thus any freesurfer > > program) can read will do, you don't need dicom. Try giving trac-all the > > phase difference maps you have and let's see what happens. > > > > Best, > > a.y > > > > On Wed, 16 Jul 2014, Eileen Moore wrote: > > > > > Hi Anastasia, > > > > > > OK - our imaging physicists had developed a wrapper script around > > epidewarp > > > which takes our dicom images and converts them into the phase > difference > > map > > > (it is based on the script that was authored by Doug Greve for the > fBIRN > > > consortium). It looks like the tracula script requires dicom images. Is > > > there a way for me to do epidewarp manually and then follow through > with > > the > > > remaining steps using trac-all? > > > > > > Thanks, > > > Eileen. > > > > > > > > > Date: Mon, 14 Jul 2014 11:23:47 -0400 (EDT) > > > From: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > > > Subject: Re: [Freesurfer] trac-all -prep error field map error > > > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > > > Message-ID: > > > <alpine.LRH.2.03.1407141119560.23459(a)nmr.mgh.harvard.edu> > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > > Hi Eileen - That step is run with the program epidewarp.fsl, > > > which you can > > > run on the command line to see the available options. The input > > > phase map > > > volume is expected to have either 2 frames (2 separate phase > > > maps) or 1 > > > frame (the difference phase map). This error from trac-all means > > > that it > > > found that your input phase map has something other than 1 or 2 > > > frames, so > > > it doesn't know how to handle it. > > > > > > Hope this helps, > > > a.y > > > > > > On Sat, 12 Jul 2014, Eileen Moore wrote: > > > > > > > Hi - I'm using freesurfer 5.3 on an Ubuntu operating system. > > > I'm tyring to > > > > run tracula on some? images acquired from a GE scanner. I am > > > running into > > > > problems when I try to perform the registration-based > > > B0-inhomogeneity > > > > compensation, getting an error in the terminal output: "ERROR: > > > Unrecognized > > > > format of phase map". However, trac-all -prep runs fine when I > > > skip the > > > > B0-inhomogeneity compensation step. Is there something else I > > > need to do to > > > > use field map correction? > > > > > > > > I've attached the trac-all.log and a copy of the terminal > > > output. > > > > > > > > Thanks, > > > > Eileen. > > > > > > > > > > > > > > > > > > > > > > > > > > > >

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Re: [Freesurfer] longitudinal QDEC help
by Martin Reuter 05 Sep '14

05 Sep '14

Hi Taylor, You can do the glmfit osgm on whatever you like (rate, percentchange pc1, or symm. percent change spc). I recommend SPC. The 2stage model page shows an example of glmfit with osgm flag and explains how to stack your data first. Best Martin Sent via my smartphone, please excuse brevity. <div>-------- Original message --------</div><div>From: Taylor North <taylornorth189(a)hotmail.ca> </div><div>Date:09/04/2014 11:14 PM (GMT-05:00) </div><div>To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> </div><div>Subject: Re: [Freesurfer] longitudinal QDEC help </div><div> </div>Hi Martin Yes I that definitely clears things up, thanks very much for the help. As for the QCAHCE we did use the long_mris_slopes described in the tutorial you linked in your email. Just to confirm I believe I should be using the mri_glmfit -osgm model for my one sample group mean analysis and then when I want to compare against my continuous/dependent variables I should be using QDEC? Also it looks like mri_glmfit -osgm calculates % change, so should I be analyzing % change, not symmetrized percent change on my QDEC analysis as well, even though it say symmetrized percent change is the more robust result? Thanks again for your help Taylor From: mreuter(a)nmr.mgh.harvard.edu Date: Thu, 4 Sep 2014 22:44:16 -0400 To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] longitudinal QDEC help Hi Taylor, first, in your description you mention 'base and 6 month'. Better call it 'baseline' or 'first and second time points at 0 and 6 months' in order to not confuse the first time point with the 'base' = within-subject template created as the second step. I think you did not confuse it, but just want to make sure. From your description it is not clear how you computed the symmetrized percent change. You say you ran QCACHE, but how? Did you use long_mris_slopes as described here: http://freesurfer.net/fswiki/LongitudinalTwoStageModel http://freesurfer.net/fswiki/FsTutorial/LongitudinalTutorial That step computes slopes for each subject and (instead of having 2 thickness maps) reduces the information to a single map (here the symmetrized percent change is simply: 100 * tp2-tp1/(0.5*(tp1+tp2)) ) . These maps are stored in the base directories (one for each subject and of corse each hemisphere that you run). Now to your questions: 1) I think a 'one sample group mean' analysis is not possible in QDEC. For that you have to use mri_glmfit -osgm …. I wish we had this functionality and I'll see how hard it would be to implement it in future versions of QDEC (this came up frequently and it should not be too hard). 2) a) the longitudinal qdec table use the cross id's in the fsid column for simplicity. When it is used in many programs (e.g. long_mris_slopes, long_stats_slopes and other scripts with the long-qdec option) the scripts knows that it is a longitudinal qdec table (because of the existing fsid-base column) and internally use the longitudinal directories for processing. The cross sectional directories are never used. b) as mentioned above, the results from the first stage analysis (creation of the within subject slopes and percent changes) are stored in the base directories. They are used in this step and found there. (and you are right, the recon-all results from the base should not be analyzed directly, but here the data that is used is derived from the longitudinal directories and just placed in the base so that it can be found for each subject). Hope that explains it. Best, Martin On Sep 4, 2014, at 9:33 PM, Taylor North <taylornorth189(a)hotmail.ca> wrote: Hello, I am having some troubles using QDEC to analyze the cortical thickness changes in my group study and I was hoping someone may be able to give me a hand. The steps I have done are as follows: I am working on a study looking at 40 subjects scanned at two time points (base and 6 months after). I have followed all the steps for longitudinal processing for each subject (cross,base, and longitudinals) and made edits where they were necessary to the base. I then entered all 40 subjects into a QDEC table as follows fsid fsid-base time gender age crosstpN1 base1 0 female 20 crosstpN2 base1 6 female 20 .......... continues for rest of the subjects then I ran the QCHACHE on the data, made a Qdecrc. file in the subject DIR, and then transformed the longitudinal QDEC table into a QDEC table which looks like: fsid time gender age Base1 3 female 20 .......... continues for the rest of the subjects. I then followed the QDEC steps outlined In the group tutorial. (import cross sectional table, generate stats data table, import aseg volume, set longitudinal dependent variables and pick continuous variable. 1) the first problem I am having is that when I go to process the longitudinal group results through QDEC it makes me pick a continuous variable when I just want to analyze the dependent variable The symmetrized percent change. So I have tried picking different continuous variables ( such as age or importing rhcortex volume etc...) with choosing symmetrized percent change as the dependent variable. No matter what continuous variable I pick the question: ``does the average symmetrized percent change differ from zero"? always comes up, the problem is depending on what continuous variable I pick the results change. Is there a way to just look at the longitudinal thickness changes across a group alone, because I first want to look at the atrophy across the whole group over 6 months and then compare the differences in atrophy against the diagnosed and non diagnosed group. 2) another thing I don't quite understand is it seems like the longitudinal qdec tables are made with the cross of the subjects under fsid, but why wouldn't you use the longitudinals under the fsid for the longitudinal table instead? Also it seems like in the cross sectional qdec table the base is the subject being analyzed under fsid, which also doesn't make sense to me because in the tutorial it says base should not be used directly for analysis. thanks for the help! Taylor _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --------------------------------- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu _______________________________________________ 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.

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longitudinal QDEC help
by Taylor North 04 Sep '14

04 Sep '14

Hello, I am having some troubles using QDEC to analyze the cortical thickness changes in my group study and I was hoping someone may be able to give me a hand. The steps I have done are as follows: I am working on a study looking at 40 subjects scanned at two time points (base and 6 months after). I have followed all the steps for longitudinal processing for each subject (cross,base, and longitudinals) and made edits where they were necessary to the base. I then entered all 40 subjects into a QDEC table as follows fsid fsid-base time gender age crosstpN1 base1 0 female 20 crosstpN2 base1 6 female 20 .......... continues for rest of the subjects then I ran the QCHACHE on the data, made a Qdecrc. file in the subject DIR, and then transformed the longitudinal QDEC table into a QDEC table which looks like: fsid time gender age Base1 3 female 20 .......... continues for the rest of the subjects. I then followed the QDEC steps outlined In the group tutorial. (import cross sectional table, generate stats data table, import aseg volume, set longitudinal dependent variables and pick continuous variable. 1) the first problem I am having is that when I go to process the longitudinal group results through QDEC it makes me pick a continuous variable when I just want to analyze the dependent variable The symmetrized percent change. So I have tried picking different continuous variables ( such as age or importing rhcortex volume etc...) with choosing symmetrized percent change as the dependent variable. No matter what continuous variable I pick the question: ``does the average symmetrized percent change differ from zero"? always comes up, the problem is depending on what continuous variable I pick the results change. Is there a way to just look at the longitudinal thickness changes across a group alone, because I first want to look at the atrophy across the whole group over 6 months and then compare the differences in atrophy against the diagnosed and non diagnosed group. 2) another thing I don't quite understand is it seems like the longitudinal qdec tables are made with the cross of the subjects under fsid, but why wouldn't you use the longitudinals under the fsid for the longitudinal table instead? Also it seems like in the cross sectional qdec table the base is the subject being analyzed under fsid, which also doesn't make sense to me because in the tutorial it says base should not be used directly for analysis. thanks for the help! Taylor

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Freesurfer September 2014