Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Qdec and 3 groups GLM
by Lena Palaniyappan 07 Jan '11

07 Jan '11

I have a single factor with three levels (diagnosis) and trying to setup qdec, but I get the following message - I have a .levels file with all 3 groups specified - the contrasts are not getting generated automatically. Data table loading completed successfully. SUBJECTS_DIR is '/Volumes/FREECOM/Applications/freesurfer/subjects/conn' ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels ninputs = 87 Checking inputs nframestot = 87 Allocing output Done allocing nframes = 87 Writing to /Volumes/FREECOM/Applications/freesurfer/subjects/conn/qdec/Untitled/y.mgh gdfReadHeader: reading /Volumes/FREECOM/Applications/freesurfer/subjects/conn/qdec/Untitled/qdec.fsgd INFO: gd2mtx_method is dods Reading source surface /Volumes/FREECOM/Applications/freesurfer/subjects/conn/fsaverage/surf/lh.white ERROR: no contrasts specified. Error in Analyze: command failed: mri_glmfit --y /Volumes/FREECOM/Applications/freesurfer/subjects/conn/qdec/Untitled/y.mgh --fsgd /Volumes/FREECOM/Applications/freesurfer/subjects/conn/qdec/Untitled/qdec.fsgd dods --glmdir /Volumes/FREECOM/Applications/freesurfer/subjects/conn/qdec/Untitled --surf fsaverage lh --label /Volumes/FREECOM/Applications/freesurfer/subjects/conn/fsaverage/label/lh.aparc.label Any help? Thanks Lena ________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH 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 use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

2 1

variance or stdev from average
by Thesen, Thomas 07 Jan '11

07 Jan '11

Hi, I am using mris_average_curvature to create an average thickness map across subjects (registered to fsaverage). The command line I am running is: mris_average_curvature lh.thickness lh sphere.reg subj01 subj02 .... subj20 outputfile This produces the average, but my question is if there a way to also create a measure of variability at the vertex level from that group, e.g. the associated variance or standard deviation? Thanks, Thomas </PRE> <html> <body> ------------------------------------------------------------<br /> This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.<br /> ================================= </body> </html> <PRE>

3 2

mkanalysis-sess and -TER
by Yuko Yotsumoto 07 Jan '11

07 Jan '11

Hi all, (-------- freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0 --------) I created sequences for event-related design, using optseq2. optseq2 --ntp 150 --tr 2 --psdwin 0 20 1 --ev TG1 2 22 --ev IG1 2 22 --ev CNT 2 22 --ev TGIG 2 22 --ev TGCN 2 22 --nsearch 2000 --focb nCB10pt --nkeep 15 --o MO Then, I did: preproc-sess -df sessdirfile -s MO01B -fwhm 5 -fsd bold mkanalysis-sess -analysis fmcsm5TER1 -TR 2 -paradigm para.para -designtype event-related -funcstem fmcsm5 -motioncor -runlistfile runfile6 -inorm -polyfit 2 -mcextreg -nconditions 5 -timewindow 20 -prestim 4 -TER 1 -autostimdur -force mkcontrast-sess -analysis fmcsm5TER1 -contrast AllNull -a 1 -a 2 -a 3 -a 4 -a 5 -c 0 selxavg3-sess -s MO01B -df sessdirfile -analysis fmcsm5TER1 -overwrite -TER in mkanalysis-sess doesn't seem to be working correct (see the right picture in the link). when I set -TER for mkanalysis-sess to be 2, the plot looks fine (see the left picture in the link). http://www.nmr.mgh.harvard.edu/~yuko/images/HDR_TER2_TER1.jpg Does this mean the sequence I used wasn't good for -TER=1? Or is there a way to make the plot right? Yuko

2 1

ICV and adjusting watershed
by L.Hoekstra＠psy.umcn.nl 07 Jan '11

07 Jan '11

Dear Freesurfer users, We were suprised to find out in two cases that after adjusting watershed (because of skull that was left) and autorecon2 and autorecon3, the ICV was exactly the same as the ICV measured by pipeline--> autorecon-all. If we didn't adjust watershed in one case the skull was included in the pial. Did we had to rerun autorecon 1 after adjusting watershed to get the skull out of the ICV measure? thx, Liesbeth Hoekstra Het UMC St Radboud staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud University Nijmegen Medical Centre is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

2 1

.label file for each ROI?
by Ingalhalikar, Madhura 06 Jan '11

06 Jan '11

Hi, I am trying to implement FSL and freesurfer to compute structural adjacency matrix. The webpage http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_surface.html has been a major help. I just have one question. When I use probtrackx for fiber tracking, I have to seed the cortical ROI's and subcortical structres one by one. In this case, how can I create a .label file for each cortical and subcortical ROI;s ? Thanks for your help, Madhura The information contained in this e-mail message is intended only for the personal and confidential use of the recipient(s) named above. If the reader of this message is not the intended recipient or an agent responsible for delivering it to the intended recipient, you are hereby notified that you have received this document in error and that any review, dissemination, distribution, or copying of this message is strictly prohibited. If you have received this communication in error, please notify us immediately by e-mail, and delete the original message.

2 3

black background to white in tksurfer
by Ritobrato Datta 06 Jan '11

06 Jan '11

Is there a way to set the black background to white in tksurfer ? Thanks Ri

1 0

Using aseg to sample other image types
by Carl Anderson 06 Jan '11

06 Jan '11

Dear Freesurfer, I have co-registered a map of whole brain T2-relaxation time values to the corresponding aseg.mgz for this subject (see attached jpegs). Does a tool exist in freesurfer to enable regional sampling of T2 values from the T2-relaxation time map based on aseg? Thanks for any thoughts. Happy New Year. <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School & The Neuroimaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972; Fax: 617-855-2770 e-mail: remfract(a)gmail.com; carl_anderson(a)hms.harvard.edu <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>

3 3

Volume for a range of slices
by Tyler Blazey 06 Jan '11

06 Jan '11

Hi, Is there any way to return the volume for a specific range of slices using the tools offered by FreeSurfer? I tried using mri_convert on aseg.mgz to select the slices I needed, and then running mri_segstats on the resulting volume. For example: mri_convert --slice-crop 1 122 aseg.mgz aseg_1_122.mgz mri_convert --slice-crop 123 255 aseg.mgz aseg_123_255.mgz mri_convert --slice-crop 1 122 norm.mgz norm_1_122.mgz mri_convert --slice-crop 123 255 norm.mgz norm_123_255.mgz mri_segstats --seg aseg_1_122.mgz --pv norm_1_122.mgz --sum ~/Desktop/1_122.txt --ctab $FREESURFER_HOME/ASegStatsLUT.txt --id 17 --subject tblaze mri_segstats --seg aseg_123_255.mgz --pv norm_123_255.mgz --sum ~/Desktop/123_255.txt --ctab $FREESURFER_HOME/ASegStatsLUT.txt --id 17 --subject tblaze When I look at the output, however, the total volume for the the ROI (left hippocampus in this case) for the two split volumes (4536 mm3) does not equal the value in aseg.stats (4543 mm3). I have tried using different slice ranges and different versions of FreeSurfer (4.5, 5.0), and I always have the same problem. Is there something that I am doing incorrectly that accounts for this discrepancy? Or is there a better way to do all this? Thanks, as always, for any replies. - Tyler Blazey

3 4

changing tkmedit keyboard shortcuts
by Mehul Sampat 05 Jan '11

05 Jan '11

Hi Folks, In tkmedit, to toggle between the main and aux volumes, one uses "ctrl-1" and "ctrl-2". I would like to change this to just "1" and "2" Is it possible to do so using tkmedit scripting ? If yes, could you tell me which function argument I should change ? I looked at the tkmedit scripting help page ( https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditReference/TkM… ) but i dont know which function argument to change. Thanks Mehul

2 1

rotate and reslice anatomical volume
by Rosa Lafer-Sousa 05 Jan '11

05 Jan '11

Hi, I need to manually rotate and reslice an anatomical volume. I am pretty sure this can be done using tkregister (or tkregister2?), but the documentation is limited. If tkregister is the way to go, what is the command line I need to enter pull up my volume (e.g raw_rawavg.mgz) in the GUI? If tkregister is not the way to go, what is? thanks! Rosa ---- Rosa Lafer-Sousa Lab Manager, Bevil Conway Wellesley College - Neuroscience 106 Central Street Wellesley, MA 210-325-3185 rlaferso(a)wellesley.edu

3 3

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