FREESURFER-7.1: recon-all exited with error "ERROR: cannot find or read transforms/talairach.m3z"
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Dear Freesurfer,
Using Freesurfer version 7.1, I was running recon-all on 13 subjects, using the command below ls *.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
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 below ls *.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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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:
External Email - Use CautionDear Freesurfer,
Using Freesurfer version 7.1, I was running recon-all on 13 subjects, using the command below ls *.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
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 mailto: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:External Email - Use Caution Dear Freesurfer, Using Freesurfer version 7.1, I was running recon-all on 13 subjects, using the command below ls *.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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 256x146x256 and voxal size is 1x1.2x1 mm i downloaded as T1 (ticked button) from PPMI, and also visually looks ok
Regards,
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:
External Email - Use CautionThank 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:
External Email - Use CautionDear Freesurfer,
Using Freesurfer version 7.1, I was running recon-all on 13 subjects, using the command below ls *.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
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Sure, send us a .nii volume that fails and we will take a look Bruce
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 256x146x256 and voxal size is 1x1.2x1 mm i downloaded as T1 (ticked button) from PPMI, and also visually looks ok
Regards,
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:
External Email - Use CautionThank 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: External Email - Use Caution
Dear Freesurfer,
Using Freesurfer version 7.1, I was running recon-all on 13 subjects, using the command below ls *.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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
You can use these commands
From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu It will ask you for a user name: use "anonymous" (no quotes) It will ask you for a password: use "anonymous" (no quotes) cd transfer/incoming binary put subject.tar.gz Send an email that the file has been and the name of the file.
On 5/20/2020 12:08 AM, Bruce Fischl wrote:
Sure, send us a .nii volume that fails and we will take a look Bruce
On May 19, 2020, at 11:38 PM, Safi Ullah . safi.ullah@uog.edu.pk wrote:
External Email - Use Caution
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 256x146x256 and voxal size is 1x1.2x1 mm i downloaded as T1 (ticked button) from PPMI, and also visually looks ok
Regards,
Safi
On Wed, May 20, 2020 at 11:27 AM Douglas N. Greve <dgreve@mgh.harvard.edu mailto: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:External Email - Use Caution 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 <mailto: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:External Email - Use Caution Dear Freesurfer, Using Freesurfer version 7.1, I was running recon-all on 13 subjects, using the command below ls *.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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas N. Greve -
Safi Ullah .