Re: [Freesurfer] Resampling from MNI 152 to MNI 305 - Problem with orientation

Hi Balaji, fslswapdim (a command line program which comes as part of fsl) should solve your orientation problems. If you have fsl installed (which you should do!) then typing fslswapdim input_volume_name -x output_volume_name into the terminal should swap RAS to LAS and vice versa. Or you can jus

Re: [Freesurfer] Adding a new measure to the design tab

Hi Jeanette, Which version of FreeSurfer are you running. Also, can you try renaming the qdec.Qdecrc to .Qdecrc and try again. Here's more info on editing the .Qdecrc file with the new measures. https://surfer.nmr.mgh.harvard.edu/fswiki/.Qdecrc Sita. On Mon, 13 Jun 2011, Jeanette Berberich w

[Freesurfer] Talairach Transformation failed on Freesurfer 5.1

Dear Freesurfer users, I got different transformation matrices (shown below) when running ver 5.0 and ver 5.1 on the same subject - ver 5.0 was doing great but ver 5.1 failed: I would appreciate it if you can give me some advice. Yi-Yu Chou

Re: [Freesurfer] make_average_subject error in T1.mgz and t1.mgz

that's weird. I'm not sure what to do. The log says that it is creating T1.mgz and not t1.mgz. Can you try this: cd $SUBJECTS_DIR/subject/mri mri_normalize -g 1 nu.mgz T1.mgz this should create T1.mgz and not t1.mgz doug tulu wrote: > Dear FS experts and Prof. Douglas N Greve, > Here is log

Re: [Freesurfer] Resampling from MNI 152 to MNI 305 - Problem with orientation

To go from mni152 to the MNI305 2mm space, use mri_vol2vol --mov mni305.2mm.nii.gz \ --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \ --reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat \ --inv --o output.mni305.2mm.nii.gz This will resample MNI152_T1_2mm.nii.gz (or anyt

Re: [Freesurfer] trac-all - bedp errors

Hi Deryk , Thanks for checking...As Anastasia mentioned, If FSL's bedpostx runs well then that should work as well...I'm not exactly sure about why the error is coming up and I can't replicate it on my computer either. Can you check one more thing in your terminal? In your dmri.bedpostX directory

Re: [Freesurfer] Resampling from MNI 152 to MNI 305 - Problem with orientation

Thanks for the response! I seem to be getting better results. I was wondering if there was any way the same resampling can be achieved using Freesurfer 4.5 since a lot of analysis (including analysis with other tasks) has already been done in it, or if it is okay to use JUST the reg.2mm.mni152.dat

Re: [Freesurfer] Talairach Transformation failed on Freesurfer 5.1

is this the talairach.xfm? On Tue, 14 Jun 2011, Yiyu Chou wrote: > Dear Freesurfer users, > > I got different transformation matrices (shown below) when running ver 5.0 > and ver 5.1 on the same subject > - ver 5.0 was doing great but ver 5.1 failed: > I would appreciate it if you can give me som

Re: [Freesurfer] Talairach Transformation failed on Freesurfer 5.1

a change in 5.1 over 5.0 is that in 5.1 the talairach stage takes orig.mgz as input, whereas in 5.0 and prior, it used nu.mgz as input. (this was done so that the nu correction stage could make use of the talairach.xfm). you can either: - add the flag -use-mritotal to the end of recon-all to hav

Re: [Freesurfer] Talairach Transformation failed on Freesurfer 5.1

Thank you, Nick This is much appreciated !! It works now and the talairach.xfm is: 1.08349275588989 -0.0557942688465118 -0.0535474419593811 3.1632091999054 0.0642405077815056 1.0216326713562 0.235359072685242 -13.4880638122559 0.0452854037284851 -0.281521290540695 1.20965027809143 16.36351203918

[Freesurfer] error in *recon-all -all -s* and *qdec*

Hello, Freesurfers, When I use *recon-all -all -s ...* there exists the error *mris_volmask.bin: error while loading shared libraries: /usr/local/freesurfer//lib/vtk/lib/vtk-5.2/libvtkRendering.so.5.2: cannot restore segment prot after reloc: Permission denied* Would you please tell me how to sol

Re: [Freesurfer] Resampling from MNI 152 to MNI 305 - Problem with orientation

You should be able to use the reg and mni305.2mm.nii.gz in 4.5 doug On 6/14/11 12:25 PM, Balaji Goparaju wrote: Thanks for the response! I seem to be getting better results. I was wondering if there was any way the same resampling can be achieved using Freesurfer 4.5 since a lot of analysis (i

Re: [Freesurfer] error in *recon-all -all -s* and *qdec*

what version of freesurfer is being run? that error is from an old version (prior to v4.5 i think). i suggest updating to v5.1. n. On Wed, 2011-06-15 at 08:52 +0800, Sophy Zhu wrote: > Hello, Freesurfers, > > When I use *recon-all -all -s ...* > there exists the error *mris_volmask.bin: error

[Freesurfer] Tracula - error in pre-proc

Hi, I do the pre-processing with the following command: trac-all -prep -c ./scripts/dmrirc_single_subject THe process exits with error when it comes to fslroi (attached pls find the log file). I try to re-run the fslroi command as follow: fslroi /autofs/space/guasha_001/users/phoebe/strab_func

Re: [Freesurfer] mri_ca_register error

Hi Bruce, It was a RAM issue, I only had 1 G for the virtual machine, put it to it's max which I think is 1.7 on a 4G machine. Worked! Thanks! Cheers, Vanessa -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Thursday, 2 June 2011 10:31 a.m. To: Vanessa L

Re: [Freesurfer] mri_ca_register error

Glad to hear it Bruce On Jun 14, 2011, at 10:45 PM, Vanessa Lim wrote: > Hi Bruce, > > It was a RAM issue, I only had 1 G for the virtual machine, put it to it's > max which I think is 1.7 on a 4G machine. Worked! Thanks! > Cheers, > Vanessa > > -Original Message- > From: Bruce Fi