Re: [Freesurfer] Qdec table

Nathan, Here are the steps I use to create QDEC dat files on a Mac: -Export/save your data in SPSS/Excel as a .csv file -Open the .csv file in TextWrangler (a free text editor for Mac) -Do a Find & Replace of the "," for " " to make it a space separated file -Down at the bottom of the TextWran

Re: [Freesurfer] slopes of interaction analysis in tksurfer

Hard to say. Can you send me the fsgd file? Stefan Brauns wrote: > Thank you for your fast response. > > According to the vertex on the overlay map, there are differences in > the slopes of "red" and "blue" groups, that are not close to 0. One > can also see in the picture of the first mail, tha

Re: [Freesurfer] ICV for incomplete whole brain coverage

that does look pretty good. My guess iss that the eTIV is also fine for this volume as it's only a 12 parameter transform, but I could be wrong (since I already was about our ability to accurately label this type of acquisition!) Bruce On Tue, 17 Nov 2009, Juranek, Jenifer wrote: > Hi Bruce, >

Re: [Freesurfer] slopes of interaction analysis in tksurfer

what do you mean by "see the slopes"? Those lines have a slope (it just looks like it is close to 0). Not sure why you can't see all 16, might be a limit in the fsgd visualization. Stefan Brauns wrote: > Hi all, > > I have done an analysis of thickness and a neuropsych variable as a > covariate

Re: [Freesurfer] Qdec table

Some programs notoriously add Ctrl-M at the end of every line ( or every cell ) If you have the vi editor you can follow this method http://www.tech-recipes.com/rx/150/remove-m-characters-at-end-of-lines-in-vi/ to remove all the instances of Ctrl-M and again try in qdec. Unfortunately I am

Re: [Freesurfer] Qdec table

Unfortunately I'm not running windows. Are you familiar with any tricks I can use on a mac? On 11/17/09 5:15 PM, "Douglas N Greve" wrote: If you're creating the file in windows, try running dos2unix on the file. doug Dankner, Nathan (NIH/NIMH) [F] wrote: > Hi all, > > I am attempting to cre

Re: [Freesurfer] Qdec table

If you're creating the file in windows, try running dos2unix on the file. doug Dankner, Nathan (NIH/NIMH) [F] wrote: > Hi all, > > I am attempting to create a qdec.table.dat file, and have been unable to find > a way to paste my data into it in a way that will make it readable. When I > paste

[Freesurfer] Qdec table

Hi all, I am attempting to create a qdec.table.dat file, and have been unable to find a way to paste my data into it in a way that will make it readable. When I paste it in qdec always outputs an error when trying to open it, even if visually the file appears to be correct. Is there an easy w

[Freesurfer] recon - local directory

Dear Freesurfer users, I don't have privileges to create directories in freesurfer installation folder as i am using freesurfer from server. So i am not able to run "recon-all -s Desktop/test/sub1/vol1.mgz -autorecon1" giving a path name to a folder in Desktop where my image volume is stored.

Re: [Freesurfer] edits to pial surface

you'll need to either add control points and/or edit the wm.mgz On Tue, 17 Nov 2009, Dana W. Moore wrote: > Hi Bruce, > > Thanks for the suggestion. Which function should I use to fix > segmentation/topology errors? > > Thanks, > Dana > > At 10:24 AM 11/17/2009, Bruce Fischl wrote: >> Hi Dana,

Re: [Freesurfer] Best way to convert Philips par/rec to mgz

I think you can just run mri_convert, passing it one dicom file from the series, eg mri_convert one.dcm 001.mgz this will preserve the resolution. doug Julie McEntee wrote: > Hello, > > I have T1-weighted data from Philips 3 T scanner obtained at a > resolution of 0.898 X 0.898 X 0.9 mm in bo

Re: [Freesurfer] edits to pial surface

Hi Bruce, Thanks for the suggestion. Which function should I use to fix segmentation/topology errors? Thanks, Dana At 10:24 AM 11/17/2009, Bruce Fischl wrote: >Hi Dana, > >what's the bright stuff out near the pial surface? Is it dura? It's >hard to tell from just a single slice. If it is, the

[Freesurfer] Best way to convert Philips par/rec to mgz

Hello, I have T1-weighted data from Philips 3 T scanner obtained at a resolution of 0.898 X 0.898 X 0.9 mm in both dicom (8 bit) and par/rec (pixel size = int16) format. I would like to preserve the acquisition resolution of the data in par/rec format; what is the best way to convert such data to

Re: [Freesurfer] Average brain error

And does the "getpwdcmd: command not found" still occur? Anna Rotarska-Jagiela wrote: > When I type which getpwdcmd, I get: > /apps/prod/i686/freesurfer-4.4.0/fsfast/bin/getpwdcmd > And I checked, the file is there. > > Anna > > > 2009/11/17 Douglas N Greve > >

Re: [Freesurfer] Average brain error

When I type which getpwdcmd, I get: /apps/prod/i686/freesurfer-4.4.0/fsfast/bin/getpwdcmd And I checked, the file is there. Anna 2009/11/17 Douglas N Greve > What happens when you type > > which getpwdcmd > > And can you see the file in $FREESURFER_HOME/fsfast/bin? > > Anna Rotarska-Jagiela wr

Re: [Freesurfer] tkmedit

but the volume needs to be in the subjects's mri dir. Alternatively, you can use -f to path to it directly. That is: tkmedit f- Desktop/test/sub1/vol1.mgz cheers, Bruce On Tue, 17 Nov 2009, Douglas N Greve wrote: > You should not use the -f option with the subject/volume option. Try > using -a

Re: [Freesurfer] Clusterwise Correction for Multiple Comparisons error

Looks like it did not find any vertices above the threshold that you used for the simulation (though it should give a better error msg). Before you run the simulation, you can look at the map at your given threshold. If there are no vertices above threshold, then nothing is going to show up in

Re: [Freesurfer] tkmedit

You should not use the -f option with the subject/volume option. Try using -aux instead. Rajagopalan, Venkateswaran wrote: > > Hello, > > I am new to freesurfer, i having the following problem. I placed my > subject's data in folder "Desktop/test/sub1/vol1.mgz". I used "tkmedit > sub1 vol1 -f $

Re: [Freesurfer] FreeSurferColorLUT for FSL

Sorry, I have not. Let us know if you get it to work. doug Nasim Maleki wrote: > Dear all, > > I would like to view the aparc.a2009s+aseg files in FSL and therefore > I need to make LUTs for FSL from the FreeSurferColorLUT. I was just > curious to know if any of you has ever done this and if

Re: [Freesurfer] reply

Sorry, add --inv to the cmd line Jared Price wrote: > Doug, I tried mri_vol2vol --mov .../orig/001.mgz --targ ...orig/001.mgz > --regheader -o ...This created a volume but the same issue > remained. When I load a segmentation on top of the created volume, > tkmedit won't let me alter the s

[Freesurfer] Clusterwise Correction for Multiple Comparisons error

I am trying to do the clusterwise correction for multiple comparisons and came upon a problem that maybe someone can help me with. ri_volcluster --in brianweisinger/g1g2.intercept/sig.mgh --csd brianweisinger/csd/mc-z.negative.j001-g1g2.intercept.csd --mask brianweisinger/mask.mgh --cwsig bri

Re: [Freesurfer] Average brain error

What happens when you type which getpwdcmd And can you see the file in $FREESURFER_HOME/fsfast/bin? Anna Rotarska-Jagiela wrote: > Dear Doug, > thank you for your response. The path you named is added. Is there > anything else we can check? > Anna > > 2009/11/16 Douglas N Greve

[Freesurfer] tkmedit

Hello, I am new to freesurfer, i having the following problem. I placed my subject's data in folder "Desktop/test/sub1/vol1.mgz". I used "tkmedit sub1 vol1 -f $bme/home..Desktop/test" the following command to open and view my image and i get the following error " bme undefined variable. What i

Re: [Freesurfer] ICV for incomplete whole brain coverage

Hi Jenifer, how much is missing? If a substantial amount I would think things would fail, including the segmentation itself, but we very rarely do this. Bruce On Tue, 17 Nov 2009, Juranek, Jenifer wrote: > A colleague asked me to look at some T1s for possible Freesurfer analyses. > Unfortunat

[Freesurfer] ICV for incomplete whole brain coverage

A colleague asked me to look at some T1s for possible Freesurfer analyses. Unfortunately, several subjects do not have whole brain acquisitions (I know, quite unexpected and disappointing). Would it be possible to correct volumes of subcortical structures (which are covered by the acquisition) f

Re: [Freesurfer] extract aparc.anot area

Hi Grégory In the 2005 version of the sulco-gyral based atlas, you should find a label called "transverse temporal gyrus" that correspond to the most anterior one that is supposed to correspond to primary auditory cortex ; when posterior one(s) was(ere) present it(they) was(were) included into

[Freesurfer] moving 001.mgz to anatomical space

I see the mistake I made. Works well now. Thanks for the help. Jared ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] FreeSurferColorLUT for FSL

Dear all, I would like to view the aparc.a2009s+aseg files in FSL and therefore I need to make LUTs for FSL from the FreeSurferColorLUT. I was just curious to know if any of you has ever done this and if there is an easy way around it. Thanks for your help in advance, Nasim ___

[Freesurfer] extract aparc.anot area

Hi everyone, I need to draw Heschl gyri on freesurfer pial surface of my subjects but it’s not easy because this area is not directly visible. So: 1. Is there a simple mean to cut the surface to see more internal areas with freesurfer tools (or other???) ? 2. Is it possible to extract only de

Re: [Freesurfer] edits to pial surface

Hi Dana, what's the bright stuff out near the pial surface? Is it dura? It's hard to tell from just a single slice. If it is, then you could try erasing it. Looks like there were also segmentation/topology fixing errors in the right superior temporal gyrus, which you could fix. Finally, you can

[Freesurfer] follow-up

...Also, I should mention that slice thickness in the MRI acquisition sequence was 1.3 mm so the native voxels are not 1x1x1. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] reply

Doug, I tried mri_vol2vol --mov .../orig/001.mgz --targ ...orig/001.mgz --regheader -o ...This created a volume but the same issue remained. When I load a segmentation on top of the created volume, tkmedit won't let me alter the segmentation. If I use "new segmentation" as opposed to load

Re: [Freesurfer] Average brain error

Dear Doug, thank you for your response. The path you named is added. Is there anything else we can check? Anna 2009/11/16 Douglas N Greve > Try adding $FREESURFER_HOME/fsfast/bin to your path. > > > doug > > Anna Rotarska-Jagiela wrote: > > > > > > Dear Freesurfer Users, > > during the creation