[Freesurfer] problems converting to nii

Hi, I am running FreeSurfer version 3.01 and am trying to convert some .mgz files to *.nii format. When I run >mri_convert in_vol.mgz out_vol.nii or >mri_convert -ot nii in_vol.mgz out_vol.nii mri_convert runs without errors but the resulting .nii file cannot be opened by AFNI. Do you know how I ca

[Freesurfer] N3 in FreeSurfer

Is the normalization software called N3 a standard part of the dev release of Freesurfer? Michele ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] mri_ca_normalize error

Hi, mri_ca_normalize failed for a subject. Here is the CA normalize portion of recon-all.log: === CA Normalize Thu Nov 17 17:02:05 PST 2005 $SUBJECTS_DIR//mri mri_ca_normalize -mask brain.mgz nu.mgz /space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64/avera

[Freesurfer] T1 volume problem

Hi, I am having problems with the dev version of Freesurfer. I realized after viewing the aseg that there was a skullstrip problem that I hadn't noticed when I checked the brain volume between -autorecon1 and -autorecon2. When I open brain.mgz and T1.mgz in tkmedit, they look identical (i.e. I ca

[Freesurfer] -autorecon1/-autorecon2

Hi, I'm using version "freesurfer-Linux-centos4.0_x86_64-dev20050921-full". After recon-all ... -autorecon1, the skull is stripped but a decent portion of the meninges remain. I tried using recon-all -skullstrip -wsthresh -subjid I ran that with h=20, h=10 and h=2. It didn't seem to help so I

[Freesurfer] Freesurfer output question

Hi, I have some questions (sent to me by someone else, actually) about freesurfer output from make_cortex_table.csh. 1. Do integrated_rectified_mean_curvature & integrated_rectified_Gaussian_curvature refer to the shape/arc of the surface of the cortex either before or after inflation? Or are t

[Freesurfer] talairach transform problem

I ran recon-all -stage1 -nomotioncor -subjid It exited with errors during mri_fill: mri_fill: could not find corpus callosum No such file or directory INFO: Modifying dst c_(r,a,s), using the transform dst INFO: Modifying dst c_(r,a,s), using the transform dst find_cutting_plane:seed point not in

[Freesurfer] mri_convert with *.IMG

Hi, I was given some MRI structural data originally scanned on a GE Signa 5. It was converted from Genesis to 8-bit *.tif's and 16-bit *.IMG's (with corresponding *.HDR files). The raw data is 256 pixels x 256 pixels x 2 bytes, little endian Intel. There are 124 .TIF, .IMG and .HDR files I have t

[Freesurfer] COR to BRIK

Hi, Is there a way to view an aseg with colors in afni once it has been converted to .img? Michele ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] reconstruction problem

I am trying to recon a sagittal T1 series from a functional scan, originally in AFNI format. I converted it to COR using mri_convert -it brik /path/to/.BRIK $SUBJECTS_DIR/subjid/mri/orig The first run of recon-all -stage1 (-nomotioncor) exited with errors (mri_fill exited with non-zero status).

[Freesurfer] mri_normalize & mri_fill

I'm still having problems... With control points saved, I did in : mri_normalize -f $SUBJECTS_DIR//tmp/control.dat -no1d $SUBJECTS_DIR//mri/orig $SUBJECTS_DIR//mri/T1 Then I ran recon-all -stage1 -nomotioncor -subjid subjid and got: . . . Intensity Normalization Fri Jun 3 12:26:01 PDT 2005 $SUB

[Freesurfer] mri_normalize question

I'm trying to do a recon on a subject with a brain tumor. mri_normalize exited with non-zero status so -stage1 exited with errors. I tried running -stage1 with -usecontrolpoints (using 7 wm points) and it still failed. Then I tried running it with -nonormalization and got an error because there

[Freesurfer] aseg skull strip failed

What is the best way to correct an aseg when non-brain regions (eg the skull) are labelled? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] recon-all -stage1 sharpen_volume

When I run recon-all -stage1 -subjid , it exits after the following: - Nu Intensity Correction Fri Mar 18 17:19:49 PST 2005 mri_convert orig nu0.mnc mri_convert orig nu0.mnc reading from orig... TR=2730.00, TE=3.31, TI=1000.00, flip angle=7.00 i_ras = (-

[Freesurfer] nu_correct problem

I'm having problems with recon-all. It used to work but recently, every time I've used it, I get a nu_correct error. I don't think we have had any freesurfer upgrades since the last time recon-all worked. Here's the log. Anyone know what's wrong? ip07:mperry[12] setenv SUBJECTS_DIR ip07:mper