Freesurfer

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30132 discussions

epidewarp
by Marco Loggia, PhD 25 Aug '11

25 Aug '11

Dear Surfers, In the past couple of days epidewarp.fsl has been failing, reporting "vsm-smooth: Command not found" (see below). Epidewarp was run using the same parameters, and within the same script that I have been using with no problems for many months... Has there been a software update that I have missed? Thanks, Marco >> >> Marco >> >> >> bash-3.2$ /usr/local/freesurfer/stable/bin/epidewarp.fsl --mag >> $dirpath/$subjdir/fieldmap/fieldmap1.nii --dph >> $dirpath/$subjdir/fieldmap/fieldmap2.nii --epi bold.nii --tediff 2.54 >> --esp .48 --sigma 2 --vsm shiftmap --epidw bold_dw.nii >> FSLVersion 4.1.5 >> FSLVerMaj 4 >> Logfile is shiftmap.log >> FSLOUTPUTTYPE NIFTI >> Extension is nii >> nframes = 180, nmidframe = 90 >> fslroi /autofs/cluster/randy/2/cuff_FM/CuffFM_FM039/6min_rest/bold.nii >> ./tmp-epidewarp.26204.fsl/exf.nii 90 1 >> fslroi /autofs/cluster/randy/2/cuff_FM/CuffFM_FM039/fieldmap/fieldmap1.nii >> ./tmp-epidewarp.26204.fsl/mag 0 1 >> bet ./tmp-epidewarp.26204.fsl/mag.nii ./tmp-epidewarp.26204.fsl/brain.nii >> fslmaths ./tmp-epidewarp.26204.fsl/brain.nii -bin >> ./tmp-epidewarp.26204.fsl/brain.nii >> fslmaths ./tmp-epidewarp.26204.fsl/brain.nii -dilM >> ./tmp-epidewarp.26204.fsl/head.nii >> fslmaths ./tmp-epidewarp.26204.fsl/head.nii -dilM >> ./tmp-epidewarp.26204.fsl/head.nii >> fslmaths ./tmp-epidewarp.26204.fsl/head.nii -dilM >> ./tmp-epidewarp.26204.fsl/head.nii >> fslmaths >> /autofs/cluster/randy/2/cuff_FM/CuffFM_FM039/fieldmap/fieldmap2.nii -sub >> 2047.5 -mul 0.00153435539 ./tmp-epidewarp.26204.fsl/dph -odt float >> prelude -p ./tmp-epidewarp.26204.fsl/dph -a >> ./tmp-epidewarp.26204.fsl/mag.nii -o ./tmp-epidewarp.26204.fsl/dph -f -v >> -m ./tmp-epidewarp.26204.fsl/head.nii >> Loading volumes >> Phase loaded >> Magnitude loaded >> Mask loaded >> Number of phase splits = 8 >> Calculating starting matrices (5173 by 5173) >> Finished connection_matrices >> 13289 constraints left >> 7990 constraints left >> 6210 constraints left >> 4125 constraints left >> 2042 constraints left >> 174 constraints left >> Did while loop 5172 times >> fslmaths ./tmp-epidewarp.26204.fsl/dph -mul 0 >> ./tmp-epidewarp.26204.fsl/ph.zeros.nii >> fslmerge -t ./tmp-epidewarp.26204.fsl/ph.nii >> ./tmp-epidewarp.26204.fsl/ph.zeros.nii ./tmp-epidewarp.26204.fsl/dph >> Masking with ./tmp-epidewarp.26204.fsl/brain.nii >> fugue -i ./tmp-epidewarp.26204.fsl/mag.nii -u >> ./tmp-epidewarp.26204.fsl/magdw.nii -p ./tmp-epidewarp.26204.fsl/ph.nii >> --dwell=.48 --asym=2.54 --mask=./tmp-epidewarp.26204.fsl/brain.nii >> --saveshift=./tmp-epidewarp.26204.fsl/vsmmag.nii --smooth2=2 >> VSM Mean is -0.110589 >> fslmaths ./tmp-epidewarp.26204.fsl/vsmmag.nii -sub -0.110589 >> ./tmp-epidewarp.26204.fsl/vsmmag.nii >> fslmaths ./tmp-epidewarp.26204.fsl/vsmmag.nii -mul >> ./tmp-epidewarp.26204.fsl/brain.nii ./tmp-epidewarp.26204.fsl/vsmmag.nii >> fugue -i ./tmp-epidewarp.26204.fsl/mag.nii -w >> ./tmp-epidewarp.26204.fsl/magfw.nii >> --loadshift=./tmp-epidewarp.26204.fsl/vsmmag.nii >> --mask=./tmp-epidewarp.26204.fsl/brain.nii >> flirt.fsl -in ./tmp-epidewarp.26204.fsl/magfw.nii -ref >> ./tmp-epidewarp.26204.fsl/exf.nii -out >> ./tmp-epidewarp.26204.fsl/magfw-in-exf.nii -omat >> ./tmp-epidewarp.26204.fsl/magfw-in-exf.fsl.mat -bins 256 -cost corratio >> -searchrx -10 10 -searchry -10 10 -searchrz -10 10 -dof 6 -interp >> trilinear >> flirt.fsl -in ./tmp-epidewarp.26204.fsl/vsmmag.nii -ref >> ./tmp-epidewarp.26204.fsl/exf.nii -out shiftmap -init >> ./tmp-epidewarp.26204.fsl/magfw-in-exf.fsl.mat -applyxfm >> vsm-smooth --fwhm 10 --i shiftmap --o shiftmap >> vsm-smooth: Command not found. >> >> >> ______________________ >> >> Marco L. Loggia, PhD >> Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital >> Harvard Medical School >> >> Psychiatric Neuroimaging Research Program >> CNY Building 120, suite 100 >> Charlestown, Massachusetts 02129 >> Phone: (617) 643-7267 >> Fax: (617) 643-7340 >> marco(a)nmr.mgh.harvard.edu >> >> > > ______________________________ Marco L. Loggia, PhD Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital Harvard Medical School CNY Building 120, suite 101E Charlestown, Massachusetts 02129 Phone: (617) 643-7267 Fax: (617) 643-7340 e-mail: marco(a)nmr.mgh.harvard.edu

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fsaverage
by Antonella Kis 25 Aug '11

25 Aug '11

Dear All: I wonder if for a new FSGD file (e.g. age.fsgd) the resample of each subjects data to fsaverage (into a common space), as well as concatenating all the subjects' into a single file, will change my old fsaverage. Thank you. Antonella

2 1

tracula executables for snow leopard now online
by Anastasia Yendiki 25 Aug '11

25 Aug '11

Hi all - By popular demand we've posted the dmri_* executables compiled on snow leopard here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopar… This is not the entire FS distribution, just the commands that are called by trac-all. If you are a mac user with snow leopard and have been running into memory issues with the leopard version, you can download this, copy the new files into your $FREESURFER_HOME/bin, and try rerunning the part of the analysis that had errored out. Let us know if there are any problems, a.y

4 9

Intensity normalization parameters to fix dura included in pial surface
by Martina Ly 24 Aug '11

24 Aug '11

Hello freesurfers, Dura is being included in the pial surface of the superior section of the brain in about 80% of the subjects (about 200) that I'm processing in fs version 5.1 on Mac OS X 10.6.8. The T1s were acquired on a GE 3T scanner. It takes too much time to manually edit the dura and I would not like to do so much manual intervention on the other 2 time points. Adjusting the watershed parameters and the -gcut flag did not help. Would I be able to adjust nu_correct or mri_normalize (the intensity normalization steps prior to skull stripping)? I'm also thinking of using another intensity correction software (i.e. unicorr) to put back into the freesurfer pipeline but I would prefer a flag or parameter I can adjust within fs. Any suggestions would be appreciated! Best, Martina

2 2

Procedure to get amygdalar sub-regions and brainstem Brainstem consituents volumes
by Irwin, William 24 Aug '11

24 Aug '11

Hello- In the FreeSurferColorLUT.txt,v 1.70.2.1 2011/05/02 file, there are labels for sub-regions of interest. For example amygdala and brainstem. How does one go about extracting the volumes for these regions? Thank you in advance, Wil #No. Label Name: R G B A 7001 Lateral-nucleus 72 132 181 0 7002 Basolateral-nucleus 243 243 243 0 7003 Basal-nucleus 207 63 79 0 7004 Centromedial-nucleus 121 20 135 0 7005 Central-nucleus 197 60 248 0 7006 Medial-nucleus 2 149 2 0 7007 Cortical-nucleus 221 249 166 0 7008 Accessory-Basal-nucleus 232 146 35 0 7009 Corticoamygdaloid-transitio 20 60 120 0 7010 Anterior-amygdaloid-area-AAA 250 250 0 0 7011 Fusion-amygdala-HP-FAH 122 187 222 0 7012 Hippocampal-amygdala-transition-HATA 237 12 177 0 7013 Endopiriform-nucleus 10 49 255 0 7014 Lateral-nucleus-olfactory-tract 205 184 144 0 7015 Paralaminar-nucleus 45 205 165 0 7016 Intercalated-nucleus 117 160 175 0 7017 Prepiriform-cortex 221 217 21 0 7018 Periamygdaloid-cortex 20 60 120 0 7019 Envelope-Amygdala 141 21 100 0 7020 Extranuclear-Amydala 225 140 141 0 # Label names and colors for Brainstem consituents # No. Label Name: R G B A 170 brainstem 119 159 176 0 171 DCG 119 0 176 0 172 Vermis 119 100 176 0 173 Midbrain 119 200 176 0 174 Pons 119 159 100 0 175 Medulla 119 159 200 0

2 3

Cortical Flattening
by Tax, C.M.W. 24 Aug '11

24 Aug '11

Dear Doug, Tank you for your response. The freesurfer wikipage I was following: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch Do I have to do some additional steps? Thank you in advance, Regards, Chantal

2 2

pial surfaces totally off
by Reza Farivar 24 Aug '11

24 Aug '11

Hello, I've tried a number of ways to generate pial surfaces for a monkey brain that has, to my eyes, very clear contrast. The white matter is segmented without too much pain and is mostly correct, but the pial surface never completely covers the gray matter. Instead, it either attaches to the white matter surface or meets the pial surface half way. I've tried more non-uniformity correction, and even painting in the gray matter more uniformly so that it could not possibly miss it, yet it does. Are there some secret parameters (i.e., low, hi gray values, etc. ) that one can play with it? Any guidance would be much appreciated. Cheers, Reza

1 0

Intensity normalization parameters to fix dura included in pial surface
by Martina Ly 24 Aug '11

24 Aug '11

Hello freesurfers, Dura is being included in the pial surface of the superior section of the brain in about 80% of the subjects (about 200) that I'm processing in fs version 5.1 on Mac OS X 10.6.8. The T1s were acquired on a GE 3T scanner. It takes too much time to manually edit the dura and I would not like to do so much manual intervention on the other 2 time points. Adjusting the watershed parameters and the -gcut flag did not help. Would I be able to adjust nu_correct or mri_normalize (the intensity normalization steps prior to skull stripping)? I'm also thinking of using another intensity correction software (i.e. unicorr) to put back into the freesurfer pipeline but I would prefer a flag or parameter I can adjust within fs. I've attached a tkmedit and a pial image (flattening of gyri due to including dura). Any suggestions would be appreciated! Best, Martina

1 0

.curv
by Antonella Cappelletti 24 Aug '11

24 Aug '11

Hi, I need a sulcal map and I saw that freesurfer can generate .curv and .sulc files that have this information. It is possibile to convert these formats into a vtk one, or to join the information of a .curv file format whit a volumetric one, having a volumetric file with the infomations of a .curv file? -- Antonella

2 3

Brain volume in FreeSurfer analysis
by zuzana nedelska 24 Aug '11

24 Aug '11

Hello, I have a question about calculating brain volume (in mm3) when performing recon-all. Do I take brainseg volume in the analysis stream line as subject's brain volume (in mm3)? Thank you for reply.

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