[Freesurfer] localGI - results interpretation

Dear FS users, can anybody help me in understanding the results of the localGI pipeline? After calling the recon-all -s *subj *-localGI recon-all -s *subj* -qcache -measure pial_lgi mri_segstats --annot *subj *lh aparc --i $SUBJECTS_DIR/*subj*/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats

[Freesurfer] rh.fsaverage_sym.sphere.reg

Hi all, I am now working with the 5.3 version and performing interhemispheric registration (building my own atlas) after running for all subjects: xhemireg --s subj001 surfreg --s subj001 --t fsaverage_sym --lh surfreg --s subj001 --t fsaverage_sym --xhemi --lh I have tried first iteration,

[Freesurfer] QDEC error and analysis termination during 'concatenating volumes' and different results from Monte Carlo Simulation from QDEC Command line

Dear Doug, Thanks for the quick response. I will try running the analyses on the command line. I've put the whole error message here if that is of any use and sheds any light to the problem? https://www.dropbox.com/s/1h1wzwidt3k1scu/ErrorMessage.txt Also, when I try to plot the stats tables

Re: [Freesurfer] LocalGI error {Disarmed}

Hi Marie,I've attached the log file.Thanks very much,Sarina Iwabuchi This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not

[Freesurfer] newbie questions - mri_convert+

I have an MPRAGE dicom file sequences on which I wish to run recon-all . Here is the command I am using: mri_convert DICOM_DIRECTORY SubjectName/mri/orig/001.mgz It returns immediately with the error message: corRead(): can't open file DICOM_DIRECTORY/COR-.info Your suggestions would be

Re: [Freesurfer] newbie questions - mri_convert+

Hi Don you don't need to convert the dicom series, just point recon-all at ONE file in the mprage series: recon-all -i full path and file name of one dicom file \ -s subject id -sd subject dir -all the list of labels is in $FREESURFER_HOME/FreeSurferColorLUT.txt, although it contains some

[Freesurfer] error when using -hemi flag for recon -all command

Hi Freesurfer team, I am running into an issue when I am specify the -hemi flag for the recon -all command (in this case recon -all -hemi rh). The command seems to work for the most part, except it errored at the end and seemed to be looking for a file for the other hemisphere. How do I get this

[Freesurfer] qdec error

HI freesurfer experts, I am running a qdec analysis, my first factor has 3 levels, my other 2 factors have 2 levels, I select my first and second factors and hit Analyze I get the error ? : Error in Analyze: command failed ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels

Re: [Freesurfer] missing anterior temporal lobe

Hi, I had successfully reconstructed a primate brain using fs5.3. But one part of left anterior temporal lobe was not correct, even with the accurate wm.mgz. See attached image for what I mean. Are there parameters to be used to correct this problem? Thanks,Xiaomin

Re: [Freesurfer] localGI - results interpretation

Hi Elisa, It is recommended to use lGI on a vertex-wise basis, i.e. to use qdec the same way you would for cortical thickness. To get access to pial_lgi as a measure of interest in qdec, you need to add a row with: MEASURE1 = pial_lgi in the .Qdecrc file located in your home directory.

Re: [Freesurfer] LocalGI error

On 29 Jul 2014, at 11:29, Sarina Iwabuchi wrote: Hi Marie, I've attached the log file. Thanks very much, Sarina Iwabuchi This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error,

[Freesurfer] The difference between wm.mgz and wm.seg.mgz

Dear Fs Experts, What is the difference between (wm.mgz and wm.seg.mgz)_ in the output of recon-all? i.e is wm.mgz means the whole white matter (right_left hemispheres and brain stem except the cerebellum) Thanks Mohamad ___ Freesurfer mailing list

Re: [Freesurfer] tkmedit doesn't show lines distinguishing grey and white matter

Hi Talia we need more information to help you. Have you looked at the wm.mgz? Is it accurate? What about the ?h.orig and ?h.orig.nofix surfaces? You need to track down where in the pipeline things started going wrong. cheers Bruce On Mon, 28 Jul 2014, Talia Raney wrote: Hi,I'm having

Re: [Freesurfer] LocalGI error {Disarmed}

Hi Sarina, Thanks for the log, I see better the problem. However I unfortunately don't know the answer. The lGI calls MRIread and load_mgh, and the error seems to related to load_mgh.m itself. Bruce / Doug / Nick, any guess what can yield such a switch expression must be a scalar or string

Re: [Freesurfer] LocalGI error {Disarmed}

Hmmm, I'm not sure what is going on either. The problem seems to be that the file is not getting unzipped (and so does not have anything to do with the switch statement per se). Sarina, try going into matlab and running a =

Re: [Freesurfer] The difference between wm.mgz and wm.seg.mgz

Hi Mohamad the wm.seg.mgz is the output of mri_segment and is a voxel segmentation that considers local intensities and estimated cortical geometry, but not topology. mri_pretess then takes the wm.seg.mgz and removes certain pathological voxel configurations (like corners touching) that mess

[Freesurfer] apply transform matrix to coordinates

Dear Freesurfers I want to apply the transform matrix talairach.xfm, to a set of discrete points. (in order to get mni coordinate and use template brain). These are electrodes, with coordinates in the brain.mgz space. Here is what I did following the advices from the Coordinates systems page :

Re: [Freesurfer] The difference between wm.mgz and wm.seg.mgz

the white is a region on the midline, probably ventricle, that we fill to create a closed surface for the cortical models. If you want a white matter mask you are better off extracting it from the aseg.mgz with mri_binarize -match cheers Bruce On Tue, 29 Jul 2014, Alshikho, Mohamad J.

[Freesurfer] qdec error

I'm getting the following erorr when running Qdec Analyze Model Factors: Discrete (fixed factors) ADHD_Persist MJ_group Nuisance factor: Age ERROR: matrix is ill-conditioned or badly scaled, condno = 10355.4 Possible problem with experimental design:

Re: [Freesurfer] rh.fsaverage_sym.sphere.reg

What is the command line that is failing and what is the full terminal output? doug On 07/29/2014 05:55 AM, angela.fav...@unipd.it wrote: Hi all, I am now working with the 5.3 version and performing interhemispheric registration (building my own atlas) after running for all subjects:

Re: [Freesurfer] QDEC error and analysis termination during 'concatenating volumes' and different results from Monte Carlo Simulation from QDEC Command line

On 07/29/2014 06:26 AM, Isotalus, Hanna wrote: Dear Doug, Thanks for the quick response. I will try running the analyses on the command line. I've put the whole error message here if that is of any use and sheds any light to the problem?

Re: [Freesurfer] error when using -hemi flag for recon -all command

You have to tell it not to do all the operations after the per-hemi phase. At one point, it used to be easy to do this, but I don't think anyone ever used the per-hemi operations and now it might not be possible. doug On 07/29/2014 10:40 AM, C. Paula de los Angeles wrote: Hi Freesurfer team,

Re: [Freesurfer] qdec error

you can't in QDEC. You'll have to use the command line stream doug On 07/29/2014 10:43 AM, Jon Alan Wieser wrote: HI freesurfer experts, I am running a qdec analysis, my first factor has 3 levels, my other 2 factors have 2 levels, I select my first and second factors and hit Analyze I

Re: [Freesurfer] FW: The difference between wm.mgz and wm.seg.mgz

that sounds like a problem with the registration/transformation not the mask itself. Why are you doing only translation? There will certainly be a rotation. Have you tried using bbregister for this? It's what we use, and in general works really well (so well that the MJ ported it to FSL!)

[Freesurfer] FLAIR Registration Problems

Hello, This email is related to the archived “bbregister and FLAIR” email chain posted by Kayle Sawyer on 5/23/2014 (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg36117.html). We have also been registering with FLAIR scans, and have run into a problem with approximately half

[Freesurfer] MRI_glmfit-sim error

I'm running a monte carlo sim and am getting an error: command line: mri_glmfit-sim \ --glmdir MTA_persistanceCP \ --sim mc-z 1000 1.3 mc-z.negative \ --sim-sign abs --cwpvalthresh 0.999 \ --overwrite output: cmdline mri_glmfit --y /Studies/MTA/qdec/MTA_persistanceCP/y.mgh --fsgd

Re: [Freesurfer] FW: The difference between wm.mgz and wm.seg.mgz

Hi Bruce, bbregister worked very well :) Thank you Mohamad -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, July 29, 2014 2:54 PM To: Freesurfer support list Subject: Re:

Re: [Freesurfer] MRI_glmfit-sim error

I'm not sure how that could have happened. Did you run mri_glmfit multiple times by any chance? On 07/29/2014 03:10 PM, Jon Alan Wieser wrote: I'm running a monte carlo sim and am getting an error: command line: mri_glmfit-sim \ --glmdir MTA_persistanceCP \ --sim mc-z 1000 1.3

Re: [Freesurfer] MRI_glmfit-sim error

I ran the analysis in qdec, not mri_glmfit . I did a few analyses in qdec Jon From: freesurfer-boun...@nmr.mgh.harvard.edu freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve gr...@nmr.mgh.harvard.edu Sent: Tuesday, July 29, 2014 3:48 PM

Re: [Freesurfer] MRI_glmfit-sim error

I think that could be the problem. I don't think that qdec cleans up after itself, so that is probably a contrast from another analysis. Try rerunning qdec using a different output folder, or just delete that contrast. doug On 07/29/2014 04:52 PM, Jon Alan Wieser wrote: I ran the analysis

Re: [Freesurfer] FLAIR Registration Problems

The current version of recon-all does not have any flexibility with regard to bbr. I'm developing a patch that will allow this to be fixed. Check back at the end of the week. doug On 07/29/2014 02:57 PM, Zamroziewicz, Marta Karolina wrote: Hello, This email is related to the archived

Re: [Freesurfer] rh.fsaverage_sym.sphere.reg

Hi Doug, this the command and output (here with only five subjects). thank you! make_average_subject --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only make_average_surface --out myatlas.i1 --surf-reg

Re: [Freesurfer] rh.fsaverage_sym.sphere.reg

Try adding --lh to the make_average_subject command line. Let me know if that works and I'll change the docs doug On 07/29/2014 05:13 PM, angela.fav...@unipd.it wrote: Hi Doug, this the command and output (here with only five subjects). thank you! make_average_subject --out myatlas.i1

Re: [Freesurfer] rh.fsaverage_sym.sphere.reg

ERROR: Flag --lh unrecognized. Try adding --lh to the make_average_subject command line. Let me know if that works and I'll change the docs doug On 07/29/2014 05:13 PM, angela.fav...@unipd.it wrote: Hi Doug, this the command and output (here with only five subjects). thank you!

Re: [Freesurfer] qdec error

Try removing the mean from the age. By this I mean to compute the mean age over all subjects regardless of group, then subtract the mean from all ages. doug On 07/29/2014 02:39 PM, Jon Alan Wieser wrote: I'm getting the following erorr when running Qdec Analyze Model Factors: Discrete

Re: [Freesurfer] rh.fsaverage_sym.sphere.reg

Is that all it prints out? What version of FS are you using? On 07/29/2014 05:26 PM, angela.fav...@unipd.it wrote: ERROR: Flag --lh unrecognized. Try adding --lh to the make_average_subject command line. Let me know if that works and I'll change the docs doug On 07/29/2014 05:13 PM,

Re: [Freesurfer] rh.fsaverage_sym.sphere.reg

I am using 5.3 make_average_subject --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only --lh make_average_surface --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004

Re: [Freesurfer] rh.fsaverage_sym.sphere.reg

Hi Doug, unfortunately the same error message appear... it looks for rh.fsaverage_sym.sphere.reg #@# Making rh registration template - /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1 mris_make_template -norot -annot aparc rh fsaverage_sym.sphere.reg subj001 subj001/xhemi

Re: [Freesurfer] rh.fsaverage_sym.sphere.reg

can you send the full terminal output On 07/29/2014 06:00 PM, angela.fav...@unipd.it wrote: Hi Doug, unfortunately the same error message appear... it looks for rh.fsaverage_sym.sphere.reg #@# Making rh registration template -

Re: [Freesurfer] rh.fsaverage_sym.sphere.reg

ftp ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface Connected to surfer.nmr.mgh.harvard.edu. 220-This is the Martinos Center Anonymous FTP service. Use of this site 220-shows implicit consent to our Acceptable Use Policy outlined at

Re: [Freesurfer] rh.fsaverage_sym.sphere.reg

when you run make_average_subject, you will still need the --lh doug On 07/29/2014 06:07 PM, angela.fav...@unipd.it wrote: ftp ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface Connected to surfer.nmr.mgh.harvard.edu. 220-This is the Martinos Center Anonymous

Re: [Freesurfer] Freesurfer] QDEC error and analysis termination during 'concatenating volumes'

I'm still not sure what is going on. I can run it with 2000 files, so I still suspect a memory problem. Try running it with /usr/bin/time, ie, /usr/bin/time mri_concat ... SEnd me the last line On 07/28/2014 03:24 PM, Isotalus, Hanna wrote: Dear FreeSurfer experts, Bruce/Doug, I am

Re: [Freesurfer] rh.fsaverage_sym.sphere.reg

Oh! it works now! thank you thank you thank you Angela when you run make_average_subject, you will still need the --lh doug On 07/29/2014 06:07 PM, angela.fav...@unipd.it wrote: ftp ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface Connected to

Re: [Freesurfer] Freesurfer Start Up

Hello and thanks again, Bruce, I am not sure what is going wrong here. I tried what you said and I am getting this. Isaiahs-MacBook-Pro:~ IsaiahSmith$ recon- all -i os005a1001.nii -s Practice -sd /Users/IsaiahSmith/Documents/LABData/MRIFolder/CfMRI01/CfMRI0124May2012/SRS1 -all -bash:

Re: [Freesurfer] Freesurfer Start Up

does that file exist? You don't want angle brackets around the name (the angle brackets typically mean replace this with an actual name cheers Bruce On Wed, 30 Jul 2014, Isaiah C. Smith wrote: Hello and thanks again, Bruce, I am not sure what is going wrong here. I tried what you said and

Re: [Freesurfer] Freesurfer Start Up

The command is not found. Last login: Tue Jul 29 17:42:52 on ttys001 freesurfer-Darwin-lion-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT

Re: [Freesurfer] Freesurfer Start Up

The recon-all option is no longer working and neither is the other one. I am getting an error. Isaiahs-MacBook-Pro:~ IsaiahSmith$ recon-all help ERROR: Flag help unrecognized. help Darwin Isaiahs-MacBook-Pro.local 13.3.0 Darwin Kernel Version 13.3.0: Tue Jun 3 21:27:35 PDT 2014;