Re: [Freesurfer] Perirhinal Cortex ....how?

In that case, I'll just wait the several weeks. That's great news BTW! Thanks again for all your work. Joshua - On Tue, Dec 11, 2012 at 6:12 PM, Bruce Fischl wrote: > Hi Josh > Perirhinal will be part of the upcoming 5.2 release in a few weeks. If you > can't wait, nick can probably get you a b

Re: [Freesurfer] Perirhinal Cortex ....how?

Hi Josh Perirhinal will be part of the upcoming 5.2 release in a few weeks. If you can't wait, nick can probably get you a beta Bruce On Dec 11, 2012, at 8:25 PM, Joshua Lee wrote: > Can I get thickness values for the perirhinal (posterior parahipp too > maybe???) > I came across http://surf

[Freesurfer] Perirhinal Cortex ....how?

Can I get thickness values for the perirhinal (posterior parahipp too maybe???) I came across http://surfer.nmr.mgh.harvard.edu/fswiki/PerirhinalArea35Labels but the labels download link isn't existent. I tried running the commands on that page anyway but of course it can't find the label... Thank

Re: [Freesurfer] unpacking error

Try using a lower case nii insteadof NII. doug On 12/11/2012 05:45 PM, Staples, Lindsay Katharine wrote: > Thanks- the command line is > unpacksdcmdir -src > /cluster/archive/302/siemens/TrioTim-35006-20121203-151132-241000 -targ > /autofs/space/ernie_002/users/RAW_DATA_All_Subjects/Patients_an

Re: [Freesurfer] unpacking error

Thanks- the command line is unpacksdcmdir -src /cluster/archive/302/siemens/TrioTim-35006-20121203-151132-241000 -targ /autofs/space/ernie_002/users/RAW_DATA_All_Subjects/Patients_and_Controls/Controls_32ch/San_Juan_TENC/SJT037 -cfg /autofs/space/ernie_002/users/RAW_DATA_All_Subjects/Patients_a

Re: [Freesurfer] unpacking error

Hi Lindsay, you'll have to give us more information. Tell us what the command line is and the full terminal output. thanks doug On 12/11/2012 05:20 PM, Staples, Lindsay Katharine wrote: > Hi- > > I don't know much about freesurfer other than the very basics. Can anyone > tell me why I would be

[Freesurfer] unpacking error

Hi- I don't know much about freesurfer other than the very basics. Can anyone tell me why I would be getting the following error when I run the second unpacking command? while executing "close $flfid" ("foreach" body line 149) invoked from within "foreach runcfg $unpackcfg { set Run

Re: [Freesurfer] applying distortion correction output from epi_reg in fsl to freesurfer

Hi Doug, Thanks so much for your reply and advice.   I may have missed it, but I don't see any information regarding the --vsm option in mri_vol2surf on the command line or wiki help.   Can you provide any guidance regarding the use of this option and what the format/units/etc of this vsm shoul

Re: [Freesurfer] func2roi-sess no bold/register.dat

Hi Keith, sorry, func2roi-sess is no longer used in version 5.X. Use funcroi-config, funcroi-sess, and funcroi-table-sess instead. If you run funcroi-config -help it will give you all the documentation. doug On 12/11/2012 01:02 PM, Keith Yoder wrote: > Hi all, > > I'm using FS 5.1.0, and tryi

[Freesurfer] func2roi-sess no bold/register.dat

Hi all, I'm using FS 5.1.0, and trying to do an ROI analysis. I have completed an FS-FAST pipeline, and am now trying to use func2roi-sess with accumbens masks. I have run isxconcat-sess, mri_glmfit and mri_glmfit-sim for the contrast MMA_CUE-v-CAPO_CUE and the results make sense. I extracted l

Re: [Freesurfer] Flipping an overlay

Hi Inge, below is a way to do this. But you should only use this for overlay and not try to do statistics on the results because the results will be biased because you've done something to the LH that you have not done to the RH. You will need two new programs (mris_left_right_register and mris

Re: [Freesurfer] convert size

do you want to increase the field of view and keep the same voxel size or keep the same field of view and reduce the voxel size? doug On 12/11/2012 11:42 AM, Andrea Tateo wrote: > > > Sorry if I bother you again, > actually I would like to convert from 256,128,256 to 256,256,256 and > from 181

Re: [Freesurfer] convert size

Sorry if I bother you again, actually I would like to convert from 256,128,256 to 256,256,256 and from 181,145,181 to 256,256,256. Can you tell me the complete command and not just the option. -rl if volume is 256,256,256? thank you vary much Andrea Messaggio originale

Re: [Freesurfer] Fwd: Running Tracula: trac-preproc exited with ERRORS

Thank you so much! All (?) makes sense now that I am looking at the log files. It has actually only processed 6 (out of 102). Now I am trying to figure out why it skipped the ones it did best wishes, Prerona On 10 December 2012 20:33, s0675204 wrote: > okay. i will look through the logs for a

[Freesurfer] Flipping an overlay

Hi list, I have a rh overlay (from caret) registered to fsaverage rh. I need it on fsaverage left hemi. Is there an easy way to flip an overlay? Cheers Inge ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.ed