On May 19, 2020, at 11:38 PM, Safi Ullah . <safi.ullah@uog.edu.pk> wrote:
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Thank You Sir,Below is the header info of the volume, I read in Matlab." srcbext: ''analyzehdr: []
bhdr: []
vol: [256×146×256 double]
niftihdr: [1×1 struct]
fspec: 'D:\FS_Shared\New folder\PPMI_3000_MR_sag_3D_FSPGR_BRAVO_straight__br_raw_20110322143431148_70_S102119_I224562.nii'
pwd: 'D:\Safi\Parkinson'
flip_angle: 0
tr: 0
te: 0
ti: 0
vox2ras0: [4×4 double]
volsize: [256 146 256]
height: 256
width: 146
depth: 256
nframes: 1
vox2ras: [4×4 double]
nvoxels: 9568256
xsize: 1.2000
ysize: 1.0000
zsize: 1.0000
x_r: 0.9992
x_a: 0.0283
x_s: 0.0298
y_r: -0.0204
y_a: 0.9709
y_s: -0.2386
z_r: -0.0357
z_a: 0.2378
z_s: 0.9707
c_r: 2.1796
c_a: 7.4944
c_s: -8.3277
vox2ras1: [4×4 double]
Mdc: [3×3 double]
volres: [1.0000 1.2000 1.0000]tkrvox2ras: [4×4 double]"So, the raw image size is 256x146x256and voxal size is 1x1.2x1 mmi downloaded as T1 (ticked button) from PPMI, and also visually looks okRegards,Safi_______________________________________________On Wed, May 20, 2020 at 11:27 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:Have you looked at the images? Are they T1-weighted? What is their resolution?_______________________________________________
On 5/19/2020 5:20 PM, Safi Ullah . wrote:
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Thank you Sir,I downloaded the volumes from PPMI, it is .nii, it is whole brain. Can I send you one sample volume?
On Wed, May 20, 2020, 12:33 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:
It looks like mri_ca_register failed to create the m3z. If this is failing on 13 subjects, then there is something systematically wrong. What kind of input do you have? Eg, MPRAGE? What is the resolution? Is it whole brain?_______________________________________________
On 5/19/2020 11:17 AM, Safi Ullah . wrote:
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Dear Freesurfer,
Using Freesurfer version 7.1, I was running recon-all on 13 subjects, using the command belowls *.nii | parallel -jobs 8 recon-all -s {.} -I {} -all –qcache(also checked with this one find . -name '*.nii' | parallel -j 8 recon-all -s {.} -i {} -all -qcache)but each time i face the same error as attached with the mail.I checked the transformation folder, but the said file, talairach.m3z, is not there.the error is not same for all cases, some cases showed a different errors, stating "IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH:" as attached file recon-all(2nd type).log
Regards
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