Hi,
Command: sudo chmod -R 777 freesurfer
I really thank you for the response.I tried the above command and its asking for sudo password. How can I able to know my sudo password.
Thanking you,
IPL Neurosurgery
Sent from Outlookhttp://aka.ms/weboutlook
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edu freesurfer-request@nmr.mgh.harvard.edu Sent: 11 March 2017 22:30:01 To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 157, Issue 35
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
Today's Topics:
1. Repost: tracula stats including NAs? (Jacobs H (NP)) 2. Re: Error viewing corrected results (Antonin Skoch) 3. MRI intensity normalize (shi yao wang) 4. Re: Error mri_surf2surf FS6 (Juergen Haenggi) 5. Error while attempting Segmentation (IPL Neurosurgery) 6. Re: Error while attempting Segmentation (Juergen Haenggi) 7. How to check if FS are processing correctly. (shi yao wang) 8. Re: Intensity normalization in longitudinal processing (Bruce Fischl) 9. Re: MRI intensity normalize (Bruce Fischl) 10. -dura_thresh (Octavian Lie)
----------------------------------------------------------------------
Message: 1 Date: Fri, 10 Mar 2017 22:39:49 +0000 From: "Jacobs H (NP)" h.jacobs@maastrichtuniversity.nl Subject: [Freesurfer] Repost: tracula stats including NAs? To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: D4E8E959.31257%h.jacobs@maastrichtuniversity.nl Content-Type: text/plain; charset="us-ascii"
Hi FreeSurfer,
I have analyzed my diffusion data using Tracula and combined the voxelwise diffusion measures across all subjects in one file (following the guidelines on the wiki). In this text file, I saw that for some of these voxels some people have NAs, so their tract is most likely shorter. I now would like to do t-tests for each voxel and plot these in freeview (as also suggested in the wiki).
Would you recommend to only take those voxels that have a value in each subject to keep the number of subjects consistent at each voxel ?
Look forward to your thoughts on this.
Best wishes Heidi
Hi
this is the admin (administrator) password. if you used any password to install FreeSurfer, try this password. or try the password used to login to your user account.
Cheers Jürgen
----------------------------------------------------------------------------------------------------- University of Zurich Dr. Jürgen Hänggi, Ph.D. Department of Psychology Division Neuropsychology Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland
0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number)
j.haenggi@psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. -----------------------------------------------------------------------------------------------------
Am 12.03.2017 um 08:55 schrieb IPL Neurosurgery:
Hi, Command: sudo chmod -R 777 freesurfer
I really thank you for the response.I tried the above command and its asking for sudo password. How can I able to know my sudo password.
Thanking you,
IPL Neurosurgery
Sent from Outlook From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edufreesurfer-request@nmr.mgh.harvard.edu Sent: 11 March 2017 22:30:01 To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 157, Issue 35
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
Today's Topics:
- Repost: tracula stats including NAs? (Jacobs H (NP))
- Re: Error viewing corrected results (Antonin Skoch)
- MRI intensity normalize (shi yao wang)
- Re: Error mri_surf2surf FS6 (Juergen Haenggi)
- Error while attempting Segmentation (IPL Neurosurgery)
- Re: Error while attempting Segmentation (Juergen Haenggi)
- How to check if FS are processing correctly. (shi yao wang)
- Re: Intensity normalization in longitudinal processing (Bruce Fischl)
- Re: MRI intensity normalize (Bruce Fischl)
- -dura_thresh (Octavian Lie)
Message: 1 Date: Fri, 10 Mar 2017 22:39:49 +0000 From: "Jacobs H (NP)" h.jacobs@maastrichtuniversity.nl Subject: [Freesurfer] Repost: tracula stats including NAs? To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: D4E8E959.31257%h.jacobs@maastrichtuniversity.nl Content-Type: text/plain; charset="us-ascii"
Hi FreeSurfer,
I have analyzed my diffusion data using Tracula and combined the voxelwise diffusion measures across all subjects in one file (following the guidelines on the wiki). In this text file, I saw that for some of these voxels some people have NAs, so their tract is most likely shorter. I now would like to do t-tests for each voxel and plot these in freeview (as also suggested in the wiki).
Would you recommend to only take those voxels that have a value in each subject to keep the number of subjects consistent at each voxel ?
Look forward to your thoughts on this.
Best wishes Heidi
Hi,
I tried the below command and it displays the result as below.
Command: sudo chmod -R 777 freesurfer
[iplneurosurgery@localhost testsample]$ sudo chmod -R 777 freesurfer [sudo] password for iplneurosurgery: chmod: cannot access ‘freesurfer’: No such file or directory [iplneurosurgery@localhost testsample]$
Thanking you,
IPL Neurosurgery
Sent from Outlookhttp://aka.ms/weboutlook
________________________________ From: IPL Neurosurgery Sent: 12 March 2017 13:25:35 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: Freesurfer Digest, Vol 157, Issue 35
Hi,
Command: sudo chmod -R 777 freesurfer
I really thank you for the response.I tried the above command and its asking for sudo password. How can I able to know my sudo password.
Thanking you,
IPL Neurosurgery
Sent from Outlookhttp://aka.ms/weboutlook
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edu freesurfer-request@nmr.mgh.harvard.edu Sent: 11 March 2017 22:30:01 To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 157, Issue 35
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
Today's Topics:
1. Repost: tracula stats including NAs? (Jacobs H (NP)) 2. Re: Error viewing corrected results (Antonin Skoch) 3. MRI intensity normalize (shi yao wang) 4. Re: Error mri_surf2surf FS6 (Juergen Haenggi) 5. Error while attempting Segmentation (IPL Neurosurgery) 6. Re: Error while attempting Segmentation (Juergen Haenggi) 7. How to check if FS are processing correctly. (shi yao wang) 8. Re: Intensity normalization in longitudinal processing (Bruce Fischl) 9. Re: MRI intensity normalize (Bruce Fischl) 10. -dura_thresh (Octavian Lie)
----------------------------------------------------------------------
Message: 1 Date: Fri, 10 Mar 2017 22:39:49 +0000 From: "Jacobs H (NP)" h.jacobs@maastrichtuniversity.nl Subject: [Freesurfer] Repost: tracula stats including NAs? To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: D4E8E959.31257%h.jacobs@maastrichtuniversity.nl Content-Type: text/plain; charset="us-ascii"
Hi FreeSurfer,
I have analyzed my diffusion data using Tracula and combined the voxelwise diffusion measures across all subjects in one file (following the guidelines on the wiki). In this text file, I saw that for some of these voxels some people have NAs, so their tract is most likely shorter. I now would like to do t-tests for each voxel and plot these in freeview (as also suggested in the wiki).
Would you recommend to only take those voxels that have a value in each subject to keep the number of subjects consistent at each voxel ?
Look forward to your thoughts on this.
Best wishes Heidi
Hi
you must be in the parent folder of the folder reesurfer or provide the full path to the folder freesurfer
Godd luck Jürgen
----------------------------------------------------------------------------------------------------- University of Zurich Dr. Jürgen Hänggi, Ph.D. Department of Psychology Division Neuropsychology Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland
0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number)
j.haenggi@psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. -----------------------------------------------------------------------------------------------------
Am 13.03.2017 um 07:36 schrieb IPL Neurosurgery:
Hi,
I tried the below command and it displays the result as below.
Command: sudo chmod -R 777 freesurfer
[iplneurosurgery@localhost testsample]$ sudo chmod -R 777 freesurfer [sudo] password for iplneurosurgery: chmod: cannot access ‘freesurfer’: No such file or directory [iplneurosurgery@localhost testsample]$
Thanking you,
IPL Neurosurgery
Sent from Outlook From: IPL Neurosurgery Sent: 12 March 2017 13:25:35 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: Freesurfer Digest, Vol 157, Issue 35
Hi, Command: sudo chmod -R 777 freesurfer
I really thank you for the response.I tried the above command and its asking for sudo password. How can I able to know my sudo password.
Thanking you,
IPL Neurosurgery
Sent from Outlook From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edufreesurfer-request@nmr.mgh.harvard.edu Sent: 11 March 2017 22:30:01 To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 157, Issue 35
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
Today's Topics:
- Repost: tracula stats including NAs? (Jacobs H (NP))
- Re: Error viewing corrected results (Antonin Skoch)
- MRI intensity normalize (shi yao wang)
- Re: Error mri_surf2surf FS6 (Juergen Haenggi)
- Error while attempting Segmentation (IPL Neurosurgery)
- Re: Error while attempting Segmentation (Juergen Haenggi)
- How to check if FS are processing correctly. (shi yao wang)
- Re: Intensity normalization in longitudinal processing (Bruce Fischl)
- Re: MRI intensity normalize (Bruce Fischl)
- -dura_thresh (Octavian Lie)
Message: 1 Date: Fri, 10 Mar 2017 22:39:49 +0000 From: "Jacobs H (NP)" h.jacobs@maastrichtuniversity.nl Subject: [Freesurfer] Repost: tracula stats including NAs? To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: D4E8E959.31257%h.jacobs@maastrichtuniversity.nl Content-Type: text/plain; charset="us-ascii"
Hi FreeSurfer,
I have analyzed my diffusion data using Tracula and combined the voxelwise diffusion measures across all subjects in one file (following the guidelines on the wiki). In this text file, I saw that for some of these voxels some people have NAs, so their tract is most likely shorter. I now would like to do t-tests for each voxel and plot these in freeview (as also suggested in the wiki).
Would you recommend to only take those voxels that have a value in each subject to keep the number of subjects consistent at each voxel ?
Look forward to your thoughts on this.
Best wishes Heidi
Dear Sir/Madam,
I tried the steps given in the below link from freesurfer wiki for error nu_correct. How can I conform that the environment variables MNI_DATAPATH and MNI_PERL5LIB point into the $FREESURFER_HOME/mni path.
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2006-July/003454.html
[iplneurosurgery@localhost /]$ fixup_mni_paths Using perl '/usr/bin/perl' Patching autocrop...(original file saved to autocrop.old) Patching field2imp...(original file saved to field2imp.old) Patching imp2field...(original file saved to imp2field.old) Patching make_template...(original file saved to make_template.old) Patching mritoself...(original file saved to mritoself.old) Patching mritotal...(original file saved to mritotal.old) Patching nu_correct...(original file saved to nu_correct.old) Patching nu_estimate...(original file saved to nu_estimate.old) Patching nu_estimate_np_and_em...(original file saved to nu_estimate_np_and_em.old) Patching nu_evaluate...(original file saved to nu_evaluate.old) Patching resample_labels...(original file saved to resample_labels.old) Patching sharpen_volume...(original file saved to sharpen_volume.old) Patching xfmtool...(original file saved to xfmtool.old) done. Here are the changes: diff autocrop autocrop.old diff field2imp field2imp.old diff imp2field imp2field.old diff make_template make_template.old diff mritoself mritoself.old diff mritotal mritotal.old diff nu_correct nu_correct.old diff nu_estimate nu_estimate.old diff nu_estimate_np_and_em nu_estimate_np_and_em.old diff nu_evaluate nu_evaluate.old diff resample_labels resample_labels.old diff sharpen_volume sharpen_volume.old diff xfmtool xfmtool.old done. Note: not all systems will require a patch, and may not show any differences. Now a test of the MNI tool 'nu_correct'... nu_correct, version 1.12.0
Usage: nu_correct [-help] [options] in.mnc out.mnc
A version number and usage message should have been displayed. [iplneurosurgery@localhost /]$ nu_correct nu_correct, version 1.12.0
Usage: nu_correct [-help] [options] in.mnc out.mnc
Now I tried the command: recon-all -s testsample -all
[iplneurosurgery@localhost testsample]$ recon-all -s testsample -all Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c INFO: SUBJECTS_DIR is /home/iplneurosurgery/Documents/freesurfer/subjects Actual FREESURFER_HOME /home/iplneurosurgery/Documents/freesurfer -rw-rw-r--. 1 iplneurosurgery iplneurosurgery 103573 Mar 13 13:33 /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/scripts/recon-all.log Linux localhost.localdomain 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux '/usr/local/freesurfer/bin/recon-all' -> '/home/iplneurosurgery/Documents/freesurfer/subjects/testsample/scripts/recon-all.local-copy' #-------------------------------------------- #@# MotionCor Mon Mar 13 14:27:53 IST 2017 Found 1 runs /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue.
cp /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig/001.mgz /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/rawavg.mgz
/home/iplneurosurgery/Documents/freesurfer/subjects/testsample
mri_convert /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/rawavg.mgz /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig.mgz --conform
mri_convert.bin /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/rawavg.mgz /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/rawavg.mgz... TR=483.49, TE=12.00, TI=0.00, flip angle=73.00 i_ras = (-0.989525, -0.140773, -0.0319737) j_ras = (0.144349, -0.962296, -0.230541) k_ras = (0.00168578, -0.232741, 0.972537) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig.mgz...
mri_add_xform_to_header -c /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/transforms/talairach.xfm /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig.mgz /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig.mgz
INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon Mar 13 14:27:58 IST 2017 /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri
mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
/home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux localhost.localdomain 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Mon Mar 13 14:27:58 IST 2017 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.8137 /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.8137/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.8137/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=483.49, TE=12.00, TI=0.00, flip angle=73.00 i_ras = (-1, 9.77889e-09, 1.16415e-09) j_ras = (5.82077e-09, 0, -1) k_ras = (1.21945e-08, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.8137/nu0.mnc...
-------------------------------------------------------- Iteration 1 Mon Mar 13 14:28:00 IST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.8137/nu0.mnc ./tmp.mri_nu_correct.mni.8137/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.8137/0/ -iterations 1000 -distance 50 nu_estimate_np_and_em: couldn't find program "spline_smooth" nu_estimate_np_and_em: couldn't find program "volume_stats" nu_estimate_np_and_em: couldn't find program "mincinfo" nu_estimate_np_and_em: couldn't find program "mincmath" nu_estimate_np_and_em: couldn't find program "mincresample" add_default_args: warning: adding default arguments for unregistered program "sharpen_volume" at /home/iplneurosurgery/Documents/freesurfer/mni/bin/nu_estimate_np_and_em line 1675. add_default_args: warning: adding default arguments for unregistered program "spline_smooth" at /home/iplneurosurgery/Documents/freesurfer/mni/bin/nu_estimate_np_and_em line 1679. add_default_args: warning: adding default arguments for unregistered program "mincresample" at /home/iplneurosurgery/Documents/freesurfer/mni/bin/nu_estimate_np_and_em line 1679. add_default_args: warning: adding default arguments for unregistered program "resample_labels" at /home/iplneurosurgery/Documents/freesurfer/mni/bin/nu_estimate_np_and_em line 1679. add_default_args: warning: adding default arguments for unregistered program "mincmath" at /home/iplneurosurgery/Documents/freesurfer/mni/bin/nu_estimate_np_and_em line 1679. [iplneurosurgery@localhost.localdomain:/home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/] [2017-03-13 14:28:00] running: /home/iplneurosurgery/Documents/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.8137/0/ ./tmp.mri_nu_correct.mni.8137/nu0.mnc ./tmp.mri_nu_correct.mni.8137/nu1.imp
spawn: exec of mincinfo failed: Permission denied nu_estimate_np_and_em: crashed while running mincinfo (termination status=65280) nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) ERROR: nu_correct Linux localhost.localdomain 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s testsample exited with ERRORS at Mon Mar 13 14:28:00 IST 2017
I also tried with the command : sudo chmod -R 777 freesurfer
iplneurosurgery@localhost /]$ sudo chmod -R 777 freesurfer [sudo] password for iplneurosurgery: chmod: cannot access ‘freesurfer’: No such file or directory
kindly suggest us with solutions. Since I'm new to Freesurfer if you give some detailed steps will be appreciated much.
Thanking you,
IPL Neurosurgery
Sent from Outlookhttp://aka.ms/weboutlook
________________________________ From: IPL Neurosurgery Sent: 13 March 2017 12:06:15 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: Freesurfer Digest, Vol 157, Issue 35
Hi,
I tried the below command and it displays the result as below.
Command: sudo chmod -R 777 freesurfer
[iplneurosurgery@localhost testsample]$ sudo chmod -R 777 freesurfer [sudo] password for iplneurosurgery: chmod: cannot access ‘freesurfer’: No such file or directory [iplneurosurgery@localhost testsample]$
Thanking you,
IPL Neurosurgery
Sent from Outlookhttp://aka.ms/weboutlook
________________________________ From: IPL Neurosurgery Sent: 12 March 2017 13:25:35 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: Freesurfer Digest, Vol 157, Issue 35
Hi,
Command: sudo chmod -R 777 freesurfer
I really thank you for the response.I tried the above command and its asking for sudo password. How can I able to know my sudo password.
Thanking you,
IPL Neurosurgery
Sent from Outlookhttp://aka.ms/weboutlook
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edu freesurfer-request@nmr.mgh.harvard.edu Sent: 11 March 2017 22:30:01 To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 157, Issue 35
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
Today's Topics:
1. Repost: tracula stats including NAs? (Jacobs H (NP)) 2. Re: Error viewing corrected results (Antonin Skoch) 3. MRI intensity normalize (shi yao wang) 4. Re: Error mri_surf2surf FS6 (Juergen Haenggi) 5. Error while attempting Segmentation (IPL Neurosurgery) 6. Re: Error while attempting Segmentation (Juergen Haenggi) 7. How to check if FS are processing correctly. (shi yao wang) 8. Re: Intensity normalization in longitudinal processing (Bruce Fischl) 9. Re: MRI intensity normalize (Bruce Fischl) 10. -dura_thresh (Octavian Lie)
----------------------------------------------------------------------
Message: 1 Date: Fri, 10 Mar 2017 22:39:49 +0000 From: "Jacobs H (NP)" h.jacobs@maastrichtuniversity.nl Subject: [Freesurfer] Repost: tracula stats including NAs? To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: D4E8E959.31257%h.jacobs@maastrichtuniversity.nl Content-Type: text/plain; charset="us-ascii"
Hi FreeSurfer,
I have analyzed my diffusion data using Tracula and combined the voxelwise diffusion measures across all subjects in one file (following the guidelines on the wiki). In this text file, I saw that for some of these voxels some people have NAs, so their tract is most likely shorter. I now would like to do t-tests for each voxel and plot these in freeview (as also suggested in the wiki).
Would you recommend to only take those voxels that have a value in each subject to keep the number of subjects consistent at each voxel ?
Look forward to your thoughts on this.
Best wishes Heidi
freesurfer@nmr.mgh.harvard.edu
-
IPL Neurosurgery -
Juergen Haenggi