Freesurfer February 2013

freesurfer@nmr.mgh.harvard.edu

136 participants
236 discussions

Freesurfer 5.2 CentOS 4 aparcstats2table error
by Garikoitz Lerma-Usabiaga 11 Feb '13

11 Feb '13

Hi fs experts, I have this error every time I try tu run aparcstats2table : File "/home/glerma/fs/52/freesurfer/bin/aparcstats2table", line 221 with open(o.qdec, 'rb') as f: ^ SyntaxError: invalid syntax it appears each time I run aparcstats2table, even when I write: aparcstats2table --help I have changed the environment variables in order to run the 5.1 version, and it works as always. What else should I check? thanks! Gari

2 7

glmfit-sim trouble
by Gabriel Gonzalez Escamilla 11 Feb '13

11 Feb '13

1 0

mc-sess Error
by Daniel Cole 11 Feb '13

11 Feb '13

Hello Freesurfers, I'm encountering an error when trying to run the following commands. The command: "csh set SESSIONDIRECTORY = $FUNCTIONALS_DIR set SUBJECTDIRECTORY = $SUBJECTS_DIR set SESSIONNAME = VGP03_151211 set ANATRUNFORREG = 002 mc-sess -s $SESSIONNAME -d $SESSIONDIRECTORY -fsd bold" ---------------------------------------------------------------- This is my error log: ">> >> >> >> >> >> >> >> >> >> >> >> >> INFO: northog = 6, pct = 100 >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> ??? Undefined function or method 'fast_svbslice' for input arguments of type 'struct'. Error in ==> MRIwrite at 83 err = fast_svbslice(mri.vol,fstem,[],outbext,bmri);" Any ideas or suggestions would be greatly appreciated! -- Daniel Cole University of Rochester Brain and Cognitive Sciences dcole10(a)u.rochester.edu

2 1

Temporal lobes not included
by Kristina Nalbandian 11 Feb '13

11 Feb '13

Hello, I am trying to run cortical thickness on a few scans. After the initial recon-all -all command not all regions of grey and white matter were included. I have attached a picture of the problem (the right side temporal lobe is not included, but the the left side is). I tried adding control points and re-running the process with the command "-autorecon-all -autorecon2-cp -autorecon3 -subjid *subject name" *but I do not get a very improved result. If there anything else I can try? Thank you for all your help, Kristina Nalbandyan Neuroscience Undergraduate Interdepartmental Program, UCLA

4 5

A question regarding a "nii-read" error I get when running a script for FA values output
by Rotem Saar 11 Feb '13

11 Feb '13

Hi, My name is Rotem, I'm a PhD. student and recently started to work with freesurfer software (freesurfer-Linux-centos4-stable-pub-v5.1.0). QUESTION For several weeks, I have been trying to operate a script for FA values, with no success, and would really appreciate your help with shading some light regarding the problem and it's solution. I have a data set, after an anatomical segmentation (file is attached, named "Anatomical segmentation for fs", this is the script I'm using for brain anatomical segmentation). What I'm trying to run now is the DTI script, in which I run commands that at least for my understanding spouse to give me at the end a table with all the FA values for each brain region (ROI). The script I'm using to do this is attached and called "DTI_RUN_NEW_FOR_FS". *After running phase 5*, in which a mask file should be created (indeed I have checked and the file is created in the same folder it should be): fmri4-P67A-D3-B3:/usr/local/freesurfer/subjects> mri_mask /usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.nii /usr/local/freesurfer/subjects/FOLDER_NAME/mri/brainmask.mgz /usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii DoAbs = 0 Found 16777216 voxels in mask Writing masked volume to /usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii...done. *I run phase 6, and then get the following error message:* fmri4-P67A-D3-B3:/usr/local/freesurfer/subjects> mri_segstats --seg /usr/local/freesurfer/subjects/FOLDER_NAME/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii --sum /usr/local/freesurfer/subjects/FOLDER_NAME/stats/all_stats_fa_FOLDER_NAME $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg /usr/local/freesurfer/subjects/FOLDER_NAME/mri/wmparc.mgz --ctab /usr/local/freesurfer/FreeSurferColorLUT.txt --i usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.nii --sum /usr/local/freesurfer/subjects/FOLDER_NAME/stats/all_stats_fa_FOLDER_NAME sysname Linux hostname fmri4-P67A-D3-B3 machine i686 user fmri4 Loading /usr/local/freesurfer/subjects/FOLDER_NAME/mri/wmparc.mgz Loading usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii niiRead(): error opening file usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii ERROR: loading usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii I think the problem is between phase 5 and 6, and is related to file format (.nii) but don't have a hint regarding what can I do to solve this:( Can someone please write me the correct code line ? I would really appreciate your kind help since I run out of ideas for solutions. Thanks in advance, Rotem

2 1

Re: [Freesurfer] mean cortical thickness of significant clusters in qdec
by Douglas N Greve 11 Feb '13

11 Feb '13

It may be a German operating system replacing 1.3 with 1,3. Maybe put it in quotes, ie, "1.3" On 02/11/2013 04:17 AM, Richter, Julia wrote: > Dear Doug, > > this is what appears when I type my command in the command window: > > mri_glmfit-sim --cache 1.3 abs --cwpvalthresh .99 > ERROR: thresh 1,3, must be 1.3, 2.0, 3.0, 3.3, 4.0 > > That's it...Any ideas why this is happening? > > Many thanks in advance! > > Best, Julia > > -----Ursprüngliche Nachricht----- > Von: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] > Gesendet: Donnerstag, 7. Februar 2013 17:32 > An: Richter, Julia; Freesurfer(a)nmr.mgh.harvard.edu > Betreff: Re: AW: AW: [Freesurfer] mean cortical thickness of significant clusters in qdec > > it does not look like you changed the command line. Also, please cut and paste the info into the email instead of taking a snapshot. > thanks > doug > > On 02/04/2013 07:26 AM, Richter, Julia wrote: >> This doesn't work either (see attachment) :( >> >> -----Ursprüngliche Nachricht----- >> Von: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] >> Gesendet: Donnerstag, 31. Januar 2013 20:29 >> An: Richter, Julia; Freesurfer(a)nmr.mgh.harvard.edu >> Betreff: Re: AW: [Freesurfer] mean cortical thickness of significant >> clusters in qdec >> >> The threshold must be in the form of -log10(pthreshold). So, if you >> want pthreshold=.05, then use 1.3 doug >> >> >> >> On 01/31/2013 07:37 AM, Richter, Julia wrote: >>> Dear Doug, >>> >>> thanks for your reply. I tried the command you suggested, but I always get an error message that there is something wrong with my threshold. I took a screenshot of the command window and attached it to this mail. I will be very happy if you have a look at it. >>> >>> Looking forward to your answer, >>> >>> Best, Julia >>> >>> -----Ursprüngliche Nachricht----- >>> Von: freesurfer-bounces(a)nmr.mgh.harvard.edu >>> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von >>> Douglas Greve >>> Gesendet: Mittwoch, 30. Januar 2013 17:16 >>> An: Richter, Julia; free surfer >>> Betreff: Re: [Freesurfer] mean cortical thickness of significant >>> clusters in qdec >>> >>> Oh, sorry, I thought you said you were using mri_glmfit-sim (which >>> does not have an FDR option). Are you using the FDR in QDEC? If so, >>> it will display the voxel-wise threshold that realizes the FDR >>> threshold. You can then run mri_glmfit-sim --cache threshold sign >>> --cwpvalthresh .99 where threshold is the voxelwise threshold from >>> FDR and sign is either abs (absolute), pos, or neg. Setting >>> cwpvalthresh=.99 tell it to report all clusters >>> >>> doug >>> >>> On 1/30/13 8:09 AM, Richter, Julia wrote: >>>> No it is not...or I just do not find it. >>>> >>>> Might it be that I only get the xxx.y.ocn.dat if I correct for multiple comparisons with Monte Carlo? If yes, is there any possibility that I get this xxx.y.ocn.dat when correcting with FDR? >>>> >>>> Many thanks, Julia >>>> >>>> -----Ursprüngliche Nachricht----- >>>> Von: freesurfer-bounces(a)nmr.mgh.harvard.edu >>>> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von >>>> Douglas N Greve >>>> Gesendet: Dienstag, 29. Januar 2013 18:46 >>>> An: freesurfer(a)nmr.mgh.harvard.edu >>>> Betreff: Re: [Freesurfer] mean cortical thickness of significant >>>> clusters in qdec >>>> >>>> Hi Julia, it should just be created when mri_glmfit-sim runs. Is it not? >>>> doug >>>> >>>> >>>> On 01/29/2013 11:03 AM, Richter, Julia wrote: >>>>> Dear FreeSurfer experts, >>>>> >>>>> I did a group analysis in qdec, found several significant clusters >>>>> and would now like to extract the mean cortical thickness of each >>>>> significant cluster. I know that I have to run mri_glmfit-sim to do >>>>> this, but I do not understand which commands I need to get the >>>>> xxx.y.ocn.dat as output by running mri_glmfit-sim. >>>>> >>>>> Any ideas? Any help is appreciated. J >>>>> >>>>> Best wishes, Julia >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> Outgoing: >>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>> >>>> _______________________________________________ >>>> 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 > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

1 0

LME matlab toolbox - smooth error
by Yolanda Vives 11 Feb '13

11 Feb '13

Dear all I am a new user of the LME matlab toolbox and I have an error when running lme_lowessPlot due to the smooth function. Do I need a particular matlab toolbox to run this function? I have not seen any smooth function in the LME toolbox. Error in ==> lme_lowessPlot at 49 ybw = smooth(st,dat(ix),bw,'rlowess'); Error in ==> LME at 14 lme_lowessPlot(M(:,1),Y(:,1)+Y(:,2),0.70,M(:,2)); Thank you in advance, Yolanda

2 1

Multi-voxel pattern analysis
by Luísa Pinto 11 Feb '13

11 Feb '13

Hi, I am very new to FreeSurfer, but would like to start using it for my research. In particular, I would like to know if I could do MVPA with FreeSurfer? Thanks. Luísa

4 3

Re: [Freesurfer] Antw: Re: thickness and area in aparc.stats and mri_glmfit
by Wolff Schlotz 11 Feb '13

11 Feb '13

Very helpful, great, many thanks! Best, Wolff >>> "Anderson M. Winkler" <winkler(a)fmrib.ox.ac.uk> 11.02.2013 15:57 >>> Dear Wolff, Compared to vertexwise, analysis of regions (ROIs) have different features. If the area of true signal spans the whole region, or large parts of it, then an ROI analysis tend to be more powerful as the noise is diluted when the vertices that comprise the ROI are summed or averaged. However, ROI analyses can also be less powerful if the signal does not span the whole region, or is split across multiple regions. This alone could explain your observation. Does this help? All the best! Anderson 2013/2/11 Wolff Schlotz <Wolff.Schlotz(a)psychologie.uni-regensburg.de> Dear Anderson (and all), Many thanks for your reassuring response, but I am still puzzled about the lack of association between mean area (rh_medialorbitofrontal_area) and area in qdec (see area.png). I thought that technically there must be larger areas for vertices within medialorbitofrontal? Best wishes, Wolff >>> "Anderson M. Winkler" <winkler(a)fmrib.ox.ac.uk> 11.02.2013 14:22 >>> Dear Wolff, There is nothing wrong with your results. Your finding is one more confirmation that thickness and area are indeed different traits, which are influenced differently by different genetic and/or environmental factors, and should not be confused one with another. They represent different aspects of brain morphology and its development, and can (and should) be analyzed and interpreted each on its own right. It is also evidence that more power can be gained by using these two measurements separately, rather than mixed up as in methods that only measure gray matter volume. Assuming you did everything else correctly, your results look perfectly fine to me. All the best! Anderson 2013/2/11 Wolff Schlotz <Wolff.Schlotz(a)psychologie.uni-regensburg.de> Dear Freesurfer experts, I tested associations between a continuous predictor and thickness and area in qdec (and command line mri_glmfit, which gives the same results) and found a cluster being negatively associated with thickness orbitofrontal, but nothing for area orbitofrontal. After exporting mean thickness and area values from aparc.stats into Stata, consistent with my expectation I found a significant negative correlation with my predictor for thickness. However, I also found a significant positive association between birth weight and area. To check what might be wrong I tested correlations between mean medialorbitofrontal thickness from rh.aparc.thickness and thickness in qdec and did the same for area. As expected, large average thickness values were positively associated with thickness in medialoribotfrontal and adjacent areas (see attached qdec screenshot thickness.png), but there were no associations using area (see attached qdec screenshot area.png). My expectatioin was that there should be positive area associations similar to those for thickness. Hence my question: Is this expectation correct? If yes, why this discrepancy between thickness and area? Thank you. Wolff _______________________________________________ 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 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.

1 0

Antw: Re: thickness and area in aparc.stats and mri_glmfit
by Wolff Schlotz 11 Feb '13

11 Feb '13

Dear Anderson (and all), Many thanks for your reassuring response, but I am still puzzled about the lack of association between mean area (rh_medialorbitofrontal_area) and area in qdec (see area.png). I thought that technically there must be larger areas for vertices within medialorbitofrontal? Best wishes, Wolff >>> "Anderson M. Winkler" <winkler(a)fmrib.ox.ac.uk> 11.02.2013 14:22 >>> Dear Wolff, There is nothing wrong with your results. Your finding is one more confirmation that thickness and area are indeed different traits, which are influenced differently by different genetic and/or environmental factors, and should not be confused one with another. They represent different aspects of brain morphology and its development, and can (and should) be analyzed and interpreted each on its own right. It is also evidence that more power can be gained by using these two measurements separately, rather than mixed up as in methods that only measure gray matter volume. Assuming you did everything else correctly, your results look perfectly fine to me. All the best! Anderson 2013/2/11 Wolff Schlotz <Wolff.Schlotz(a)psychologie.uni-regensburg.de> Dear Freesurfer experts, I tested associations between a continuous predictor and thickness and area in qdec (and command line mri_glmfit, which gives the same results) and found a cluster being negatively associated with thickness orbitofrontal, but nothing for area orbitofrontal. After exporting mean thickness and area values from aparc.stats into Stata, consistent with my expectation I found a significant negative correlation with my predictor for thickness. However, I also found a significant positive association between birth weight and area. To check what might be wrong I tested correlations between mean medialorbitofrontal thickness from rh.aparc.thickness and thickness in qdec and did the same for area. As expected, large average thickness values were positively associated with thickness in medialoribotfrontal and adjacent areas (see attached qdec screenshot thickness.png), but there were no associations using area (see attached qdec screenshot area.png). My expectatioin was that there should be positive area associations similar to those for thickness. Hence my question: Is this expectation correct? If yes, why this discrepancy between thickness and area? Thank you. Wolff _______________________________________________ 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.

3 2

← Newer
1
...
14
15
16
17
18
19
20
...
24
Older →

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer February 2013