Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
Indeed we might not support running the HCP Pipelines on a windows formatted filesystem. Peace, Matt. From: "Xu, Junqian" mailto:junqian...@mssm.edu>> Date: Thursday, June 29, 2017 at 2:00 PM To: "Brown, Tim" mailto:tbbr...@wustl.edu>> Cc: "Mandelli, Maria Luisa" mailto:marialuisa.mande...@ucsf.edu>>, Matt Glasser mailto:glass...@wustl.edu>>, HCP Users mailto:hcp-users@humanconnectome.org>>, "Dierker, Donna" mailto:do...@wustl.edu>> Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found Tim, Just FYI (may not be the cause of this particular case) for completeness of your documentation, this old ticket is still open (after 6 years) for guest OS in VirtualBox. https://www.virtualbox.org/ticket/10085 Gordon On Jun 29, 2017, at 11:29 AM, Timothy B. Brown mailto:tbbr...@wustl.edu>> wrote: Hi, I'm curious to know more about the file systems in use that would cause the symbolic link operation to not be supported. I think you would be getting this "Operation not supported" error if the file system in which your SUBJECTS_DIR exists is a "non-Unix" or "non-Unix-standard" file system (maybe a "Windows" file system like FAT32 or NTFS, or some other Mac standard file system that also doesn't support symbolic links). If that is the case, moving your FREESURFER_HOME (FreeSurfer installation directory) over to the file system where your subject data is stored will not do you any good. If symbolic links are not supported on that file system, moving more files to that file system will not help. If this is the case, then moving the subject data to a file system that does support symbolic links might be a good move. Do you manage the file system that appears to be mounted at /mnt/macdata? Can you move the subject data elsewhere to a file system that does support symbolic links? Assuming that the file system in which FreeSurfer is installed is one that does support symbolic links, then moving the subject data over to that file system might be another way to alleviate the current problem. But as you wrote, you may have a space limit that prevents moving all the subject data over to that file system. If that is the case, then temporarily moving the data for a subject that is being processed through the pipelines over to the same file system on which FreeSurfer is installed might do the trick. (Move or copy the data for a subject to be processed, run the pipelines on that subject, and then move the data back to where it was.) This will, of course, add significant copying time to the beginning and end of each of your pipeline runs. Another option would be to try to take advantage of the fact that recon-all doesn't try to create the symbolic link if there is already an fsaverage directory in your .../HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w directory. Before processing the data, copy the appropriate fsaverage directory from the FreeSurfer installation directory into an fsaverage directory for your subject ($SUBJECTS_DIR/fsaverage). However, a very brief look through the recon-all script indicates that this is just one case in which it relies on being able to create a symbolic link. I haven't specifically determined if those other uses of symbolic links are ones that are invoked by the HCP Pipeline scripts. But this option would only really deal with one of those cases. It seems clear to me that recon-all is written with the expectation that your data resides on a file system that supports symbolic links. So moving in that direction (either by moving all your data to such a file system or temporarily moving the data for each subject as it is processed) is, I think, the way to go. Hope that is helpful, Tim On 06/29/2017 12:18 PM, Mandelli, Maria Luisa wrote: Hi! I think I found the problem and I saw that someone else had the same issues before when it tries to create the symbolic link it fails. Here ln -s $FREESURFER_HOME/subjects/fsaverage . ln: failed to create symbolic link `./fsaverage': Operation not supported In old post someone suggest to set the SUBJECTs_DIR to be on the same file system as $FREESURFER_HOME...I can try one case but eventually if I have more subjects I dont think I can because of space limit Let me know if you have suggestions! Thank you very much Maria Luisa Mandelli, PhD Assistant Professional Researcher University of California, San Francisco 675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158 Language Neurobiology Lab http://albalab.ucsf.edu/<https://urldefense.proofpoint.com/v2/url?u=http-3A__albalab.ucsf.edu_&d=DwMD-g&c=shNJtf5dKgNcPZ6Yh64b-A&r=QJgqxaIpHmQUddDGZ_5g0PzQF9rcc9xrheyw6Wux7DQ&m=r84iWyCg34jIRvwK7CO_gae-ZRGPsroBK8whgW_tZzs&s=ROLPfOXWSC0_55hv9n3bErVnu-N33VzigBSYSwCpUj8&e=> Memory and Aging Cent
Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
mK9fyelNaE&e=>
From: Glasser, Matthew <mailto:glass...@wustl.edu>
Sent: Wednesday, June 28, 2017 4:30:28 PM
To: Mandelli, Maria Luisa; Brown, Tim;
hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Cc: Dierker, Donna
Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
If you were to delete everything and run again do you get the same error?
Peace,
Matt.
From: "Mandelli, Maria Luisa"
mailto:marialuisa.mande...@ucsf.edu>>
Date: Wednesday, June 28, 2017 at 6:18 PM
To: Matt Glasser mailto:glass...@wustl.edu>>, "Brown, Tim"
mailto:tbbr...@wustl.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Cc: "Dierker, Donna" mailto:do...@wustl.edu>>
Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
this is the version
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-HCP
and yes I m running the HCP Pipelines
Maria Luisa Mandelli, PhD
Assistant Professional Researcher
University of California, San Francisco
675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158
Language Neurobiology Lab
http://albalab.ucsf.edu/<https://urldefense.proofpoint.com/v2/url?u=http-3A__albalab.ucsf.edu_&d=DwMD-g&c=shNJtf5dKgNcPZ6Yh64b-A&r=QJgqxaIpHmQUddDGZ_5g0PzQF9rcc9xrheyw6Wux7DQ&m=r84iWyCg34jIRvwK7CO_gae-ZRGPsroBK8whgW_tZzs&s=ROLPfOXWSC0_55hv9n3bErVnu-N33VzigBSYSwCpUj8&e=>
Memory and Aging Center
http://memory.ucsf.edu/<https://urldefense.proofpoint.com/v2/url?u=http-3A__memory.ucsf.edu_&d=DwMD-g&c=shNJtf5dKgNcPZ6Yh64b-A&r=QJgqxaIpHmQUddDGZ_5g0PzQF9rcc9xrheyw6Wux7DQ&m=r84iWyCg34jIRvwK7CO_gae-ZRGPsroBK8whgW_tZzs&s=4Q8wVST0ynfGoI38wle18-Ji588U9uvbbYu1YAzQmzM&e=>
UCSF Dyslexia Center
http://dyslexia.ucsf.edu/<https://urldefense.proofpoint.com/v2/url?u=http-3A__dyslexia.ucsf.edu_&d=DwMD-g&c=shNJtf5dKgNcPZ6Yh64b-A&r=QJgqxaIpHmQUddDGZ_5g0PzQF9rcc9xrheyw6Wux7DQ&m=r84iWyCg34jIRvwK7CO_gae-ZRGPsroBK8whgW_tZzs&s=939O-6qSoMYTDLWMAieyfxmBdMk0vrlBwmK9fyelNaE&e=>
From: Glasser, Matthew mailto:glass...@wustl.edu>>
Sent: Wednesday, June 28, 2017 4:10:27 PM
To: Mandelli, Maria Luisa; Brown, Tim;
hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Cc: Dierker, Donna
Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
That’s weird as I change the subject directory in the pipelines but don’t
normally have this error. FreeSurfer just makes a symlink. What version of
FreeSurfer are you using? Are you calling it using the HCP Pipelines?
Peace,
Matt.
From: "Mandelli, Maria Luisa"
mailto:marialuisa.mande...@ucsf.edu>>
Date: Wednesday, June 28, 2017 at 6:06 PM
To: Matt Glasser mailto:glass...@wustl.edu>>, "Brown, Tim"
mailto:tbbr...@wustl.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Cc: "Dierker, Donna" mailto:do...@wustl.edu>>
Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
Hi!thank you for your help!
the error is in the log file
Invalid argument
ERROR reading
/mnt/macdata/groups/language/malu-cloud/HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w/fsaverage/label/lh.BA1.label
Linux mmandelli-vm 3.2.0-126-virtual #169-Ubuntu SMP Fri Mar 31 14:47:56 UTC
2017 x86_64 x86_64 x86_64 GNU/Linux
So actually it s true I dont have the fsaverage directory in my subject folder
but it s in ${FREESURFER_HOME}/subjects/fsaverage
Now the my $SUBJECT_DIR is set where are my data not $FREESURFER_HOME
am I missing a link somewhere?
Maria Luisa Mandelli, PhD
Assistant Professional Researcher
University of California, San Francisco
675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158
Language Neurobiology Lab
http://albalab.ucsf.edu/<https://urldefense.proofpoint.com/v2/url?u=http-3A__albalab.ucsf.edu_&d=DwMD-g&c=shNJtf5dKgNcPZ6Yh64b-A&r=QJgqxaIpHmQUddDGZ_5g0PzQF9rcc9xrheyw6Wux7DQ&m=r84iWyCg34jIRvwK7CO_gae-ZRGPsroBK8whgW_tZzs&s=ROLPfOXWSC0_55hv9n3bErVnu-N33VzigBSYSwCpUj8&e=>
Memory and Aging Center
http://memory.ucsf.edu/<https://urldefense.proofpoint.com/v2/url?u=http-3A__memory.ucsf.edu_&d=DwMD-g&c=shNJtf5dKgNcPZ6Yh64b-A&r=QJgqxaIpHmQUddDGZ_5g0PzQF9rcc9xrheyw6Wux7DQ&m=r84iWyCg34jIRvwK7CO_gae-ZRGPsroBK8whgW_tZzs&s=4Q8wVST0ynfGoI38wle18-Ji588U9uvbbYu1YAzQmzM&e=>
UCSF Dyslexia Center
http://dyslexia.ucsf.edu/<https://urldefense.proofpoint.com/v2/url?u=http-3A__dyslexia.ucsf.edu_&d=DwMD-g&c=shNJtf5dKgNcPZ6Yh64b-A&r=QJgqxaIpHmQUddDGZ_5g0PzQF9rcc9xrheyw6Wux7DQ&m=r84iWyCg34jIRvwK7CO_gae-ZRGPsroBK8whgW_tZzs&s=939O-6qSoMYTDLWMAieyfxmBdMk0vrlBwmK
Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
Hi, I'm curious to know more about the file systems in use that would cause the symbolic link operation to not be supported. I /think/ you would be getting this "Operation not supported" error if the file system in which your SUBJECTS_DIR exists is a "non-Unix" or "non-Unix-standard" file system (maybe a "Windows" file system like FAT32 or NTFS, or some other Mac standard file system that also doesn't support symbolic links). If that is the case, moving your FREESURFER_HOME (FreeSurfer installation directory) over to the file system where your subject data is stored will not do you any good. If symbolic links are not supported on that file system, moving more files to that file system will not help. If this is the case, then moving the subject data to a file system that /does/ support symbolic links might be a good move. Do you manage the file system that appears to be mounted at /mnt/macdata? Can you move the subject data elsewhere to a file system that does support symbolic links? Assuming that the file system in which FreeSurfer is installed is one that /does/ support symbolic links, then moving the subject data over to that file system might be another way to alleviate the current problem. But as you wrote, you may have a space limit that prevents moving all the subject data over to that file system. If that is the case, then temporarily moving the data for a subject that is being processed through the pipelines over to the same file system on which FreeSurfer is installed might do the trick. (Move or copy the data for a subject to be processed, run the pipelines on that subject, and then move the data back to where it was.) This will, of course, add significant copying time to the beginning and end of each of your pipeline runs. Another option would be to try to take advantage of the fact that recon-all doesn't try to create the symbolic link if there is already an fsaverage directory in your .../HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w directory. Before processing the data, copy the appropriate fsaverage directory from the FreeSurfer installation directory into an fsaverage directory for your subject ($SUBJECTS_DIR/fsaverage). However, a very brief look through the recon-all script indicates that this is just one case in which it relies on being able to create a symbolic link. I haven't specifically determined if those other uses of symbolic links are ones that are invoked by the HCP Pipeline scripts. But this option would only really deal with one of those cases. It seems clear to me that recon-all is written with the expectation that your data resides on a file system that supports symbolic links. So moving in that direction (either by moving all your data to such a file system or temporarily moving the data for each subject as it is processed) is, I think, the way to go. Hope that is helpful, Tim On 06/29/2017 12:18 PM, Mandelli, Maria Luisa wrote: Hi! I think I found the problem and I saw that someone else had the same issues before when it tries to create the symbolic link it fails. Here ln -s $FREESURFER_HOME/subjects/fsaverage . ln: failed to create symbolic link `./fsaverage': Operation not supported In old post someone suggest to set the SUBJECTs_DIR to be on the same file system as $FREESURFER_HOME...I can try one case but eventually if I have more subjects I dont think I can because of space limit Let me know if you have suggestions! Thank you very much */Maria Luisa Mandelli, PhD/* /Assistant Professional Researcher/ *University of California, San Francisco* 675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158 Language Neurobiology Lab http://albalab.ucsf.edu/ Memory and Aging Center** _http://memory.ucsf.edu/_ UCSF Dyslexia Center http://dyslexia.ucsf.edu/ *From:* Glasser, Matthew *Sent:* Wednesday, June 28, 2017 4:30:28 PM *To:* Mandelli, Maria Luisa; Brown, Tim; hcp-users@humanconnectome.org *Cc:* Dierker, Donna *Subject:* Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found If you were to delete everything and run again do you get the same error? Peace, Matt. From: "Mandelli, Maria Luisa" <mailto:marialuisa.mande...@ucsf.edu>> Date: Wednesday, June 28, 2017 at 6:18 PM To: Matt Glasser mailto:glass...@wustl.edu>>, "Brown, Tim" mailto:tbbr...@wustl.edu>>, "hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Cc: "Dierker, Donna" mailto:do...@wustl.edu>> Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found this is the version freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-HCP and yes I m running the HCP Pipelines */Maria Luisa Mandelli, P
Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
I see ... I think I m dealing with cifs right now! we will try with a NFS area ... what could work otherwise? Maria Luisa Mandelli, PhD Assistant Professional Researcher University of California, San Francisco 675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158 Language Neurobiology Lab http://albalab.ucsf.edu/ Memory and Aging Center http://memory.ucsf.edu/ UCSF Dyslexia Center http://dyslexia.ucsf.edu/ From: Timothy Coalson Sent: Thursday, June 29, 2017 11:03:08 AM To: Mandelli, Maria Luisa Cc: Glasser, Matthew; Dierker, Donna; hcp-users@humanconnectome.org; Brown, Tim Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found Symbolic links don't require the folders to be on the same filesystem. The 'operation not supported' error seems unusual for making a symbolic link. Aside from the usual things to check (folder write permissions, whether there is already something there with that name), also know that windows and its protocols may not like symbolic links (so, if you are running this over a SMB/CIFS mount, or a FAT filesystem, or NTFS with older Linux, expect trouble). Tim On Jun 29, 2017 10:18 AM, "Mandelli, Maria Luisa" mailto:marialuisa.mande...@ucsf.edu>> wrote: Hi! I think I found the problem and I saw that someone else had the same issues before when it tries to create the symbolic link it fails. Here ln -s $FREESURFER_HOME/subjects/fsaverage . ln: failed to create symbolic link `./fsaverage': Operation not supported In old post someone suggest to set the SUBJECTs_DIR to be on the same file system as $FREESURFER_HOME...I can try one case but eventually if I have more subjects I dont think I can because of space limit Let me know if you have suggestions! Thank you very much Maria Luisa Mandelli, PhD Assistant Professional Researcher University of California, San Francisco 675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158 Language Neurobiology Lab http://albalab.ucsf.edu/ Memory and Aging Center http://memory.ucsf.edu/ UCSF Dyslexia Center http://dyslexia.ucsf.edu/ From: Glasser, Matthew mailto:glass...@wustl.edu>> Sent: Wednesday, June 28, 2017 4:30:28 PM To: Mandelli, Maria Luisa; Brown, Tim; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Cc: Dierker, Donna Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found If you were to delete everything and run again do you get the same error? Peace, Matt. From: "Mandelli, Maria Luisa" mailto:marialuisa.mande...@ucsf.edu>> Date: Wednesday, June 28, 2017 at 6:18 PM To: Matt Glasser mailto:glass...@wustl.edu>>, "Brown, Tim" mailto:tbbr...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Cc: "Dierker, Donna" mailto:do...@wustl.edu>> Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found this is the version freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-HCP and yes I m running the HCP Pipelines Maria Luisa Mandelli, PhD Assistant Professional Researcher University of California, San Francisco 675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158 Language Neurobiology Lab http://albalab.ucsf.edu/ Memory and Aging Center http://memory.ucsf.edu/ UCSF Dyslexia Center http://dyslexia.ucsf.edu/ From: Glasser, Matthew mailto:glass...@wustl.edu>> Sent: Wednesday, June 28, 2017 4:10:27 PM To: Mandelli, Maria Luisa; Brown, Tim; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Cc: Dierker, Donna Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found That’s weird as I change the subject directory in the pipelines but don’t normally have this error. FreeSurfer just makes a symlink. What version of FreeSurfer are you using? Are you calling it using the HCP Pipelines? Peace, Matt. From: "Mandelli, Maria Luisa" mailto:marialuisa.mande...@ucsf.edu>> Date: Wednesday, June 28, 2017 at 6:06 PM To: Matt Glasser mailto:glass...@wustl.edu>>, "Brown, Tim" mailto:tbbr...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Cc: "Dierker, Donna" mailto:do...@wustl.edu>> Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found Hi!thank you for your help! the error is in the log file Invalid argument ERROR reading /mnt/macdata/groups/language/malu-cloud/HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w/fsaverage/label/lh.BA1.label Linux mmandelli-vm 3.2.0-126-virtual #169-Ubuntu SMP Fri Mar 31 14:47:56 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux So actually it
Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
Symbolic links don't require the folders to be on the same filesystem. The
'operation not supported' error seems unusual for making a symbolic link.
Aside from the usual things to check (folder write permissions, whether
there is already something there with that name), also know that windows
and its protocols may not like symbolic links (so, if you are running this
over a SMB/CIFS mount, or a FAT filesystem, or NTFS with older Linux,
expect trouble).
Tim
On Jun 29, 2017 10:18 AM, "Mandelli, Maria Luisa" <
marialuisa.mande...@ucsf.edu> wrote:
Hi! I think I found the problem and I saw that someone else had the same
issues before
when it tries to create the symbolic link it fails. Here
ln -s $FREESURFER_HOME/subjects/fsaverage .
ln: failed to create symbolic link `./fsaverage': Operation not supported
In old post someone suggest to set the SUBJECTs_DIR to be on the same file
system as $FREESURFER_HOME...I can try one case but eventually if I have
more subjects I dont think I can because of space limit
Let me know if you have suggestions!
Thank you very much
*Maria Luisa Mandelli, PhD*
*Assistant Professional Researcher*
*University of California, San Francisco*
675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158
Language Neurobiology Lab
http://albalab.ucsf.edu/
Memory and Aging Center
*http://memory.ucsf.edu/ <http://memory.ucsf.edu/>*
UCSF Dyslexia Center
http://dyslexia.ucsf.edu/
--
*From:* Glasser, Matthew
*Sent:* Wednesday, June 28, 2017 4:30:28 PM
*To:* Mandelli, Maria Luisa; Brown, Tim; hcp-users@humanconnectome.org
*Cc:* Dierker, Donna
*Subject:* Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not
found
If you were to delete everything and run again do you get the same error?
Peace,
Matt.
From: "Mandelli, Maria Luisa"
Date: Wednesday, June 28, 2017 at 6:18 PM
To: Matt Glasser , "Brown, Tim" , "
hcp-users@humanconnectome.org"
Cc: "Dierker, Donna"
Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
this is the version
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-HCP
and yes I m running the HCP Pipelines
*Maria Luisa Mandelli, PhD*
*Assistant Professional Researcher*
*University of California, San Francisco*
675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158
Language Neurobiology Lab
http://albalab.ucsf.edu/
Memory and Aging Center
*http://memory.ucsf.edu/ <http://memory.ucsf.edu/>*
UCSF Dyslexia Center
http://dyslexia.ucsf.edu/
--
*From:* Glasser, Matthew
*Sent:* Wednesday, June 28, 2017 4:10:27 PM
*To:* Mandelli, Maria Luisa; Brown, Tim; hcp-users@humanconnectome.org
*Cc:* Dierker, Donna
*Subject:* Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not
found
That’s weird as I change the subject directory in the pipelines but don’t
normally have this error. FreeSurfer just makes a symlink. What version
of FreeSurfer are you using? Are you calling it using the HCP Pipelines?
Peace,
Matt.
From: "Mandelli, Maria Luisa"
Date: Wednesday, June 28, 2017 at 6:06 PM
To: Matt Glasser , "Brown, Tim" , "
hcp-users@humanconnectome.org"
Cc: "Dierker, Donna"
Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
Hi!thank you for your help!
the error is in the log file
Invalid argument
ERROR reading /mnt/macdata/groups/language/malu-cloud/HCP_project/
Pipelines_ExampleData/subjects/hcp350014/T1w/fsaverage/label/lh.BA1.label
Linux mmandelli-vm 3.2.0-126-virtual #169-Ubuntu SMP Fri Mar 31 14:47:56
UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
So actually it s true I dont have the fsaverage directory in my subject
folder but it s in ${FREESURFER_HOME}/subjects/fsaverage
Now the my $SUBJECT_DIR is set where are my data not $FREESURFER_HOME
am I missing a link somewhere?
*Maria Luisa Mandelli, PhD*
*Assistant Professional Researcher*
*University of California, San Francisco*
675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158
Language Neurobiology Lab
http://albalab.ucsf.edu/
Memory and Aging Center
*http://memory.ucsf.edu/ <http://memory.ucsf.edu/>*
UCSF Dyslexia Center
http://dyslexia.ucsf.edu/
--
*From:* Glasser, Matthew
*Sent:* Wednesday, June 28, 2017 4:00:56 PM
*To:* Brown, Tim; hcp-users@humanconnectome.org; Mandelli, Maria Luisa
*Cc:* Dierker, Donna
*Subject:* Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not
found
Perhaps I missed it but I don’t actually see the error messages you are
getting.
Peace,
Matt.
From: on behalf of "Timothy B.
Brown"
Organization: Washington University in St. Louis
Date: Wednesday, June 28, 2017 at 5:00 PM
To: "hcp-users@humanconnectome.org" , "
marialuisa.mande...@ucsf.edu"
Cc: "Dierker, Donna"
Subject: Re: [HCP-Users] pipeline struc
Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
Hi! I think I found the problem and I saw that someone else had the same issues
before
when it tries to create the symbolic link it fails. Here
ln -s $FREESURFER_HOME/subjects/fsaverage .
ln: failed to create symbolic link `./fsaverage': Operation not supported
In old post someone suggest to set the SUBJECTs_DIR to be on the same file
system as $FREESURFER_HOME...I can try one case but eventually if I have more
subjects I dont think I can because of space limit
Let me know if you have suggestions!
Thank you very much
Maria Luisa Mandelli, PhD
Assistant Professional Researcher
University of California, San Francisco
675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158
Language Neurobiology Lab
http://albalab.ucsf.edu/
Memory and Aging Center
http://memory.ucsf.edu/
UCSF Dyslexia Center
http://dyslexia.ucsf.edu/
From: Glasser, Matthew
Sent: Wednesday, June 28, 2017 4:30:28 PM
To: Mandelli, Maria Luisa; Brown, Tim; hcp-users@humanconnectome.org
Cc: Dierker, Donna
Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
If you were to delete everything and run again do you get the same error?
Peace,
Matt.
From: "Mandelli, Maria Luisa"
mailto:marialuisa.mande...@ucsf.edu>>
Date: Wednesday, June 28, 2017 at 6:18 PM
To: Matt Glasser mailto:glass...@wustl.edu>>, "Brown, Tim"
mailto:tbbr...@wustl.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Cc: "Dierker, Donna" mailto:do...@wustl.edu>>
Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
this is the version
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-HCP
and yes I m running the HCP Pipelines
Maria Luisa Mandelli, PhD
Assistant Professional Researcher
University of California, San Francisco
675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158
Language Neurobiology Lab
http://albalab.ucsf.edu/
Memory and Aging Center
http://memory.ucsf.edu/
UCSF Dyslexia Center
http://dyslexia.ucsf.edu/
From: Glasser, Matthew mailto:glass...@wustl.edu>>
Sent: Wednesday, June 28, 2017 4:10:27 PM
To: Mandelli, Maria Luisa; Brown, Tim;
hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Cc: Dierker, Donna
Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
That’s weird as I change the subject directory in the pipelines but don’t
normally have this error. FreeSurfer just makes a symlink. What version of
FreeSurfer are you using? Are you calling it using the HCP Pipelines?
Peace,
Matt.
From: "Mandelli, Maria Luisa"
mailto:marialuisa.mande...@ucsf.edu>>
Date: Wednesday, June 28, 2017 at 6:06 PM
To: Matt Glasser mailto:glass...@wustl.edu>>, "Brown, Tim"
mailto:tbbr...@wustl.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Cc: "Dierker, Donna" mailto:do...@wustl.edu>>
Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
Hi!thank you for your help!
the error is in the log file
Invalid argument
ERROR reading
/mnt/macdata/groups/language/malu-cloud/HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w/fsaverage/label/lh.BA1.label
Linux mmandelli-vm 3.2.0-126-virtual #169-Ubuntu SMP Fri Mar 31 14:47:56 UTC
2017 x86_64 x86_64 x86_64 GNU/Linux
So actually it s true I dont have the fsaverage directory in my subject folder
but it s in ${FREESURFER_HOME}/subjects/fsaverage
Now the my $SUBJECT_DIR is set where are my data not $FREESURFER_HOME
am I missing a link somewhere?
Maria Luisa Mandelli, PhD
Assistant Professional Researcher
University of California, San Francisco
675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158
Language Neurobiology Lab
http://albalab.ucsf.edu/
Memory and Aging Center
http://memory.ucsf.edu/
UCSF Dyslexia Center
http://dyslexia.ucsf.edu/
From: Glasser, Matthew mailto:glass...@wustl.edu>>
Sent: Wednesday, June 28, 2017 4:00:56 PM
To: Brown, Tim;
hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>; Mandelli,
Maria Luisa
Cc: Dierker, Donna
Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
Perhaps I missed it but I don’t actually see the error messages you are getting.
Peace,
Matt.
From:
mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of "Timothy B. Brown" mailto:tbbr...@wustl.edu>>
Organization: Washington University in St. Louis
Date: Wednesday, June 28, 2017 at 5:00 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>,
"marialuisa.mande...@ucsf.edu<mailto:ma
Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
I m trying to do that!
I ll let you know!
thank you again in the mean time
Maria Luisa Mandelli, PhD
Assistant Professional Researcher
University of California, San Francisco
675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158
Language Neurobiology Lab
http://albalab.ucsf.edu/
Memory and Aging Center
http://memory.ucsf.edu/
UCSF Dyslexia Center
http://dyslexia.ucsf.edu/
From: Glasser, Matthew
Sent: Wednesday, June 28, 2017 4:30:28 PM
To: Mandelli, Maria Luisa; Brown, Tim; hcp-users@humanconnectome.org
Cc: Dierker, Donna
Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
If you were to delete everything and run again do you get the same error?
Peace,
Matt.
From: "Mandelli, Maria Luisa"
mailto:marialuisa.mande...@ucsf.edu>>
Date: Wednesday, June 28, 2017 at 6:18 PM
To: Matt Glasser mailto:glass...@wustl.edu>>, "Brown, Tim"
mailto:tbbr...@wustl.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Cc: "Dierker, Donna" mailto:do...@wustl.edu>>
Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
this is the version
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-HCP
and yes I m running the HCP Pipelines
Maria Luisa Mandelli, PhD
Assistant Professional Researcher
University of California, San Francisco
675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158
Language Neurobiology Lab
http://albalab.ucsf.edu/
Memory and Aging Center
http://memory.ucsf.edu/
UCSF Dyslexia Center
http://dyslexia.ucsf.edu/
From: Glasser, Matthew mailto:glass...@wustl.edu>>
Sent: Wednesday, June 28, 2017 4:10:27 PM
To: Mandelli, Maria Luisa; Brown, Tim;
hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Cc: Dierker, Donna
Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
That’s weird as I change the subject directory in the pipelines but don’t
normally have this error. FreeSurfer just makes a symlink. What version of
FreeSurfer are you using? Are you calling it using the HCP Pipelines?
Peace,
Matt.
From: "Mandelli, Maria Luisa"
mailto:marialuisa.mande...@ucsf.edu>>
Date: Wednesday, June 28, 2017 at 6:06 PM
To: Matt Glasser mailto:glass...@wustl.edu>>, "Brown, Tim"
mailto:tbbr...@wustl.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Cc: "Dierker, Donna" mailto:do...@wustl.edu>>
Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
Hi!thank you for your help!
the error is in the log file
Invalid argument
ERROR reading
/mnt/macdata/groups/language/malu-cloud/HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w/fsaverage/label/lh.BA1.label
Linux mmandelli-vm 3.2.0-126-virtual #169-Ubuntu SMP Fri Mar 31 14:47:56 UTC
2017 x86_64 x86_64 x86_64 GNU/Linux
So actually it s true I dont have the fsaverage directory in my subject folder
but it s in ${FREESURFER_HOME}/subjects/fsaverage
Now the my $SUBJECT_DIR is set where are my data not $FREESURFER_HOME
am I missing a link somewhere?
Maria Luisa Mandelli, PhD
Assistant Professional Researcher
University of California, San Francisco
675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158
Language Neurobiology Lab
http://albalab.ucsf.edu/
Memory and Aging Center
http://memory.ucsf.edu/
UCSF Dyslexia Center
http://dyslexia.ucsf.edu/
From: Glasser, Matthew mailto:glass...@wustl.edu>>
Sent: Wednesday, June 28, 2017 4:00:56 PM
To: Brown, Tim;
hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>; Mandelli,
Maria Luisa
Cc: Dierker, Donna
Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
Perhaps I missed it but I don’t actually see the error messages you are getting.
Peace,
Matt.
From:
mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of "Timothy B. Brown" mailto:tbbr...@wustl.edu>>
Organization: Washington University in St. Louis
Date: Wednesday, June 28, 2017 at 5:00 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>,
"marialuisa.mande...@ucsf.edu<mailto:marialuisa.mande...@ucsf.edu>"
mailto:marialuisa.mande...@ucsf.edu>>
Cc: "Dierker, Donna" mailto:do...@wustl.edu>>
Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
Hi Maria,
My bet is that the error you are seeing is coming from the last call to
recon-all in the FreeSurferPipeline.sh script. This would be in the statements
that look like:
#Final Recon-all Steps
log_Msg "Final Recon
Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
If you were to delete everything and run again do you get the same error?
Peace,
Matt.
From: "Mandelli, Maria Luisa"
mailto:marialuisa.mande...@ucsf.edu>>
Date: Wednesday, June 28, 2017 at 6:18 PM
To: Matt Glasser mailto:glass...@wustl.edu>>, "Brown, Tim"
mailto:tbbr...@wustl.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Cc: "Dierker, Donna" mailto:do...@wustl.edu>>
Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
this is the version
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-HCP
and yes I m running the HCP Pipelines
Maria Luisa Mandelli, PhD
Assistant Professional Researcher
University of California, San Francisco
675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158
Language Neurobiology Lab
http://albalab.ucsf.edu/
Memory and Aging Center
http://memory.ucsf.edu/
UCSF Dyslexia Center
http://dyslexia.ucsf.edu/
From: Glasser, Matthew mailto:glass...@wustl.edu>>
Sent: Wednesday, June 28, 2017 4:10:27 PM
To: Mandelli, Maria Luisa; Brown, Tim;
hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Cc: Dierker, Donna
Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
That’s weird as I change the subject directory in the pipelines but don’t
normally have this error. FreeSurfer just makes a symlink. What version of
FreeSurfer are you using? Are you calling it using the HCP Pipelines?
Peace,
Matt.
From: "Mandelli, Maria Luisa"
mailto:marialuisa.mande...@ucsf.edu>>
Date: Wednesday, June 28, 2017 at 6:06 PM
To: Matt Glasser mailto:glass...@wustl.edu>>, "Brown, Tim"
mailto:tbbr...@wustl.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Cc: "Dierker, Donna" mailto:do...@wustl.edu>>
Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
Hi!thank you for your help!
the error is in the log file
Invalid argument
ERROR reading
/mnt/macdata/groups/language/malu-cloud/HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w/fsaverage/label/lh.BA1.label
Linux mmandelli-vm 3.2.0-126-virtual #169-Ubuntu SMP Fri Mar 31 14:47:56 UTC
2017 x86_64 x86_64 x86_64 GNU/Linux
So actually it s true I dont have the fsaverage directory in my subject folder
but it s in ${FREESURFER_HOME}/subjects/fsaverage
Now the my $SUBJECT_DIR is set where are my data not $FREESURFER_HOME
am I missing a link somewhere?
Maria Luisa Mandelli, PhD
Assistant Professional Researcher
University of California, San Francisco
675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158
Language Neurobiology Lab
http://albalab.ucsf.edu/
Memory and Aging Center
http://memory.ucsf.edu/
UCSF Dyslexia Center
http://dyslexia.ucsf.edu/
From: Glasser, Matthew mailto:glass...@wustl.edu>>
Sent: Wednesday, June 28, 2017 4:00:56 PM
To: Brown, Tim;
hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>; Mandelli,
Maria Luisa
Cc: Dierker, Donna
Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
Perhaps I missed it but I don’t actually see the error messages you are getting.
Peace,
Matt.
From:
mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of "Timothy B. Brown" mailto:tbbr...@wustl.edu>>
Organization: Washington University in St. Louis
Date: Wednesday, June 28, 2017 at 5:00 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>,
"marialuisa.mande...@ucsf.edu<mailto:marialuisa.mande...@ucsf.edu>"
mailto:marialuisa.mande...@ucsf.edu>>
Cc: "Dierker, Donna" mailto:do...@wustl.edu>>
Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
Hi Maria,
My bet is that the error you are seeing is coming from the last call to
recon-all in the FreeSurferPipeline.sh script. This would be in the statements
that look like:
#Final Recon-all Steps
log_Msg "Final Recon-all Steps"
recon-all -subjid $SubjectID -sd $SubjectDIR -surfvolume -parcstats -cortparc2
-parcstats2 -cortparc3 -parcstats3 -cortribbon -segstats -aparc2aseg -wmparc
-balabels -label-exvivo-ec -openmp ${num_cores} ${seed_cmd_appendix}
log_Msg "Completed"
In particular, it would be the line that is shown in red above. (Note,
depending on the version of the HCP Pipelines you are using, your version of
the recon-all command may not have the -openmp ${num_cores} or the
${seed_cmd_appendix} in it.)
The -balabels option is asking the recon-all command to "Create Brodmann area
labels by mapping from fsaverage".
You probably won
Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
this is the version
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-HCP
and yes I m running the HCP Pipelines
Maria Luisa Mandelli, PhD
Assistant Professional Researcher
University of California, San Francisco
675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158
Language Neurobiology Lab
http://albalab.ucsf.edu/
Memory and Aging Center
http://memory.ucsf.edu/
UCSF Dyslexia Center
http://dyslexia.ucsf.edu/
From: Glasser, Matthew
Sent: Wednesday, June 28, 2017 4:10:27 PM
To: Mandelli, Maria Luisa; Brown, Tim; hcp-users@humanconnectome.org
Cc: Dierker, Donna
Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
That’s weird as I change the subject directory in the pipelines but don’t
normally have this error. FreeSurfer just makes a symlink. What version of
FreeSurfer are you using? Are you calling it using the HCP Pipelines?
Peace,
Matt.
From: "Mandelli, Maria Luisa"
mailto:marialuisa.mande...@ucsf.edu>>
Date: Wednesday, June 28, 2017 at 6:06 PM
To: Matt Glasser mailto:glass...@wustl.edu>>, "Brown, Tim"
mailto:tbbr...@wustl.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Cc: "Dierker, Donna" mailto:do...@wustl.edu>>
Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
Hi!thank you for your help!
the error is in the log file
Invalid argument
ERROR reading
/mnt/macdata/groups/language/malu-cloud/HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w/fsaverage/label/lh.BA1.label
Linux mmandelli-vm 3.2.0-126-virtual #169-Ubuntu SMP Fri Mar 31 14:47:56 UTC
2017 x86_64 x86_64 x86_64 GNU/Linux
So actually it s true I dont have the fsaverage directory in my subject folder
but it s in ${FREESURFER_HOME}/subjects/fsaverage
Now the my $SUBJECT_DIR is set where are my data not $FREESURFER_HOME
am I missing a link somewhere?
Maria Luisa Mandelli, PhD
Assistant Professional Researcher
University of California, San Francisco
675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158
Language Neurobiology Lab
http://albalab.ucsf.edu/
Memory and Aging Center
http://memory.ucsf.edu/
UCSF Dyslexia Center
http://dyslexia.ucsf.edu/
From: Glasser, Matthew mailto:glass...@wustl.edu>>
Sent: Wednesday, June 28, 2017 4:00:56 PM
To: Brown, Tim;
hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>; Mandelli,
Maria Luisa
Cc: Dierker, Donna
Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
Perhaps I missed it but I don’t actually see the error messages you are getting.
Peace,
Matt.
From:
mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of "Timothy B. Brown" mailto:tbbr...@wustl.edu>>
Organization: Washington University in St. Louis
Date: Wednesday, June 28, 2017 at 5:00 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>,
"marialuisa.mande...@ucsf.edu<mailto:marialuisa.mande...@ucsf.edu>"
mailto:marialuisa.mande...@ucsf.edu>>
Cc: "Dierker, Donna" mailto:do...@wustl.edu>>
Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
Hi Maria,
My bet is that the error you are seeing is coming from the last call to
recon-all in the FreeSurferPipeline.sh script. This would be in the statements
that look like:
#Final Recon-all Steps
log_Msg "Final Recon-all Steps"
recon-all -subjid $SubjectID -sd $SubjectDIR -surfvolume -parcstats -cortparc2
-parcstats2 -cortparc3 -parcstats3 -cortribbon -segstats -aparc2aseg -wmparc
-balabels -label-exvivo-ec -openmp ${num_cores} ${seed_cmd_appendix}
log_Msg "Completed"
In particular, it would be the line that is shown in red above. (Note,
depending on the version of the HCP Pipelines you are using, your version of
the recon-all command may not have the -openmp ${num_cores} or the
${seed_cmd_appendix} in it.)
The -balabels option is asking the recon-all command to "Create Brodmann area
labels by mapping from fsaverage".
You probably won't have an fsaverage directory in the subject directory which
you are processing (in your case the
/HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w directory). In that
case, recon-all creates one for you as a symbolic link to the
$FREESURFER_HOME/subjects/fsaverage directory.
It is in a subdirectory of that created fsaverage directory that files like
lh.BA1.label should be found.
So, the first things that needs to be determined in your case are:
* At the time of this failure, does the
/HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w/fsaverage directory
exist at all?
* If it does exist, is it a symbolic link to somewhere in your FreeS
Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
That’s weird as I change the subject directory in the pipelines but don’t
normally have this error. FreeSurfer just makes a symlink. What version of
FreeSurfer are you using? Are you calling it using the HCP Pipelines?
Peace,
Matt.
From: "Mandelli, Maria Luisa"
mailto:marialuisa.mande...@ucsf.edu>>
Date: Wednesday, June 28, 2017 at 6:06 PM
To: Matt Glasser mailto:glass...@wustl.edu>>, "Brown, Tim"
mailto:tbbr...@wustl.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Cc: "Dierker, Donna" mailto:do...@wustl.edu>>
Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
Hi!thank you for your help!
the error is in the log file
Invalid argument
ERROR reading
/mnt/macdata/groups/language/malu-cloud/HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w/fsaverage/label/lh.BA1.label
Linux mmandelli-vm 3.2.0-126-virtual #169-Ubuntu SMP Fri Mar 31 14:47:56 UTC
2017 x86_64 x86_64 x86_64 GNU/Linux
So actually it s true I dont have the fsaverage directory in my subject folder
but it s in ${FREESURFER_HOME}/subjects/fsaverage
Now the my $SUBJECT_DIR is set where are my data not $FREESURFER_HOME
am I missing a link somewhere?
Maria Luisa Mandelli, PhD
Assistant Professional Researcher
University of California, San Francisco
675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158
Language Neurobiology Lab
http://albalab.ucsf.edu/
Memory and Aging Center
http://memory.ucsf.edu/
UCSF Dyslexia Center
http://dyslexia.ucsf.edu/
From: Glasser, Matthew mailto:glass...@wustl.edu>>
Sent: Wednesday, June 28, 2017 4:00:56 PM
To: Brown, Tim;
hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>; Mandelli,
Maria Luisa
Cc: Dierker, Donna
Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
Perhaps I missed it but I don’t actually see the error messages you are getting.
Peace,
Matt.
From:
mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of "Timothy B. Brown" mailto:tbbr...@wustl.edu>>
Organization: Washington University in St. Louis
Date: Wednesday, June 28, 2017 at 5:00 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>,
"marialuisa.mande...@ucsf.edu<mailto:marialuisa.mande...@ucsf.edu>"
mailto:marialuisa.mande...@ucsf.edu>>
Cc: "Dierker, Donna" mailto:do...@wustl.edu>>
Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
Hi Maria,
My bet is that the error you are seeing is coming from the last call to
recon-all in the FreeSurferPipeline.sh script. This would be in the statements
that look like:
#Final Recon-all Steps
log_Msg "Final Recon-all Steps"
recon-all -subjid $SubjectID -sd $SubjectDIR -surfvolume -parcstats -cortparc2
-parcstats2 -cortparc3 -parcstats3 -cortribbon -segstats -aparc2aseg -wmparc
-balabels -label-exvivo-ec -openmp ${num_cores} ${seed_cmd_appendix}
log_Msg "Completed"
In particular, it would be the line that is shown in red above. (Note,
depending on the version of the HCP Pipelines you are using, your version of
the recon-all command may not have the -openmp ${num_cores} or the
${seed_cmd_appendix} in it.)
The -balabels option is asking the recon-all command to "Create Brodmann area
labels by mapping from fsaverage".
You probably won't have an fsaverage directory in the subject directory which
you are processing (in your case the
/HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w directory). In that
case, recon-all creates one for you as a symbolic link to the
$FREESURFER_HOME/subjects/fsaverage directory.
It is in a subdirectory of that created fsaverage directory that files like
lh.BA1.label should be found.
So, the first things that needs to be determined in your case are:
* At the time of this failure, does the
/HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w/fsaverage directory
exist at all?
* If it does exist, is it a symbolic link to somewhere in your FreeSurfer
installation? (I believe it should be a link to the
${FREESURFER_HOME}/subjects/fsaverage directory.)
* What is the value of your FREESURFER_HOME environment variable?
Can you check into those things and let me know what you find?
Best Regards,
Tim
On 06/28/2017 09:41 AM, Mandelli, Maria Luisa wrote:
Hi!I installed the freesurfer-hcp and I got an error in the Freesurfer pipeline
here...in the label directory I dont see the file that the script is looking
for! (lh.BA1.label)
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
/usr/local/freesurfer/bin/recon-all
PWD /HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w/hcp350014/label
CMD mri_label2la
Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
Hi!thank you for your help!
the error is in the log file
Invalid argument
ERROR reading
/mnt/macdata/groups/language/malu-cloud/HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w/fsaverage/label/lh.BA1.label
Linux mmandelli-vm 3.2.0-126-virtual #169-Ubuntu SMP Fri Mar 31 14:47:56 UTC
2017 x86_64 x86_64 x86_64 GNU/Linux
So actually it s true I dont have the fsaverage directory in my subject folder
but it s in ${FREESURFER_HOME}/subjects/fsaverage
Now the my $SUBJECT_DIR is set where are my data not $FREESURFER_HOME
am I missing a link somewhere?
Maria Luisa Mandelli, PhD
Assistant Professional Researcher
University of California, San Francisco
675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158
Language Neurobiology Lab
http://albalab.ucsf.edu/
Memory and Aging Center
http://memory.ucsf.edu/
UCSF Dyslexia Center
http://dyslexia.ucsf.edu/
From: Glasser, Matthew
Sent: Wednesday, June 28, 2017 4:00:56 PM
To: Brown, Tim; hcp-users@humanconnectome.org; Mandelli, Maria Luisa
Cc: Dierker, Donna
Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
Perhaps I missed it but I don’t actually see the error messages you are getting.
Peace,
Matt.
From:
mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of "Timothy B. Brown" mailto:tbbr...@wustl.edu>>
Organization: Washington University in St. Louis
Date: Wednesday, June 28, 2017 at 5:00 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>,
"marialuisa.mande...@ucsf.edu<mailto:marialuisa.mande...@ucsf.edu>"
mailto:marialuisa.mande...@ucsf.edu>>
Cc: "Dierker, Donna" mailto:do...@wustl.edu>>
Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
Hi Maria,
My bet is that the error you are seeing is coming from the last call to
recon-all in the FreeSurferPipeline.sh script. This would be in the statements
that look like:
#Final Recon-all Steps
log_Msg "Final Recon-all Steps"
recon-all -subjid $SubjectID -sd $SubjectDIR -surfvolume -parcstats -cortparc2
-parcstats2 -cortparc3 -parcstats3 -cortribbon -segstats -aparc2aseg -wmparc
-balabels -label-exvivo-ec -openmp ${num_cores} ${seed_cmd_appendix}
log_Msg "Completed"
In particular, it would be the line that is shown in red above. (Note,
depending on the version of the HCP Pipelines you are using, your version of
the recon-all command may not have the -openmp ${num_cores} or the
${seed_cmd_appendix} in it.)
The -balabels option is asking the recon-all command to "Create Brodmann area
labels by mapping from fsaverage".
You probably won't have an fsaverage directory in the subject directory which
you are processing (in your case the
/HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w directory). In that
case, recon-all creates one for you as a symbolic link to the
$FREESURFER_HOME/subjects/fsaverage directory.
It is in a subdirectory of that created fsaverage directory that files like
lh.BA1.label should be found.
So, the first things that needs to be determined in your case are:
* At the time of this failure, does the
/HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w/fsaverage directory
exist at all?
* If it does exist, is it a symbolic link to somewhere in your FreeSurfer
installation? (I believe it should be a link to the
${FREESURFER_HOME}/subjects/fsaverage directory.)
* What is the value of your FREESURFER_HOME environment variable?
Can you check into those things and let me know what you find?
Best Regards,
Tim
On 06/28/2017 09:41 AM, Mandelli, Maria Luisa wrote:
Hi!I installed the freesurfer-hcp and I got an error in the Freesurfer pipeline
here...in the label directory I dont see the file that the script is looking
for! (lh.BA1.label)
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
/usr/local/freesurfer/bin/recon-all
PWD /HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w/hcp350014/label
CMD mri_label2label --srcsubject fsaverage --srclabel
/HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w/fsaverage/label/lh.BA1.label
--trgsubject hcp350014 --trglabel ./lh.BA1.label --hemi lh --regmethod surface
Maria Luisa Mandelli, PhD
Assistant Professional Researcher
University of California, San Francisco
675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158
Language Neurobiology Lab
http://albalab.ucsf.edu/
Memory and Aging Center
http://memory.ucsf.edu/
UCSF Dyslexia Center
http://dyslexia.ucsf.edu/
From:
hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>
<mailto:hcp-users-boun...@humanconnectome.org>
on behalf of Mandelli, Maria Luisa
<mailto:marialuisa.mande...@ucsf.edu>
Sent: Monday, June 26, 2017 1:52:02 PM
Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
Perhaps I missed it but I don’t actually see the error messages you are getting.
Peace,
Matt.
From:
mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of "Timothy B. Brown" mailto:tbbr...@wustl.edu>>
Organization: Washington University in St. Louis
Date: Wednesday, June 28, 2017 at 5:00 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>,
"marialuisa.mande...@ucsf.edu<mailto:marialuisa.mande...@ucsf.edu>"
mailto:marialuisa.mande...@ucsf.edu>>
Cc: "Dierker, Donna" mailto:do...@wustl.edu>>
Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
Hi Maria,
My bet is that the error you are seeing is coming from the last call to
recon-all in the FreeSurferPipeline.sh script. This would be in the statements
that look like:
#Final Recon-all Steps
log_Msg "Final Recon-all Steps"
recon-all -subjid $SubjectID -sd $SubjectDIR -surfvolume -parcstats -cortparc2
-parcstats2 -cortparc3 -parcstats3 -cortribbon -segstats -aparc2aseg -wmparc
-balabels -label-exvivo-ec -openmp ${num_cores} ${seed_cmd_appendix}
log_Msg "Completed"
In particular, it would be the line that is shown in red above. (Note,
depending on the version of the HCP Pipelines you are using, your version of
the recon-all command may not have the -openmp ${num_cores} or the
${seed_cmd_appendix} in it.)
The -balabels option is asking the recon-all command to "Create Brodmann area
labels by mapping from fsaverage".
You probably won't have an fsaverage directory in the subject directory which
you are processing (in your case the
/HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w directory). In that
case, recon-all creates one for you as a symbolic link to the
$FREESURFER_HOME/subjects/fsaverage directory.
It is in a subdirectory of that created fsaverage directory that files like
lh.BA1.label should be found.
So, the first things that needs to be determined in your case are:
* At the time of this failure, does the
/HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w/fsaverage directory
exist at all?
* If it does exist, is it a symbolic link to somewhere in your FreeSurfer
installation? (I believe it should be a link to the
${FREESURFER_HOME}/subjects/fsaverage directory.)
* What is the value of your FREESURFER_HOME environment variable?
Can you check into those things and let me know what you find?
Best Regards,
Tim
On 06/28/2017 09:41 AM, Mandelli, Maria Luisa wrote:
Hi!I installed the freesurfer-hcp and I got an error in the Freesurfer pipeline
here...in the label directory I dont see the file that the script is looking
for! (lh.BA1.label)
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
/usr/local/freesurfer/bin/recon-all
PWD /HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w/hcp350014/label
CMD mri_label2label --srcsubject fsaverage --srclabel
/HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w/fsaverage/label/lh.BA1.label
--trgsubject hcp350014 --trglabel ./lh.BA1.label --hemi lh --regmethod surface
Maria Luisa Mandelli, PhD
Assistant Professional Researcher
University of California, San Francisco
675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158
Language Neurobiology Lab
http://albalab.ucsf.edu/
Memory and Aging Center
http://memory.ucsf.edu/
UCSF Dyslexia Center
http://dyslexia.ucsf.edu/
From:
hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>
<mailto:hcp-users-boun...@humanconnectome.org>
on behalf of Mandelli, Maria Luisa
<mailto:marialuisa.mande...@ucsf.edu>
Sent: Monday, June 26, 2017 1:52:02 PM
To: Dierker, Donna
Cc: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
thank you very much!I have the standard Freesurfer version!
I m going to try to the HCP one now!
Maria Luisa Mandelli, PhD
Assistant Professional Researcher
University of California, San Francisco
675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158
Language Neurobiology Lab
http://albalab.ucsf.edu/
Memory and Aging Center
http://memory.ucsf.edu/
UCSF Dyslexia Center
http://dyslexia.ucsf.edu/
From: Dierker, Donna <mailto:do...@wustl.edu>
Sent: Monday, June 26, 2017 11:54:40 AM
To: Mandelli, Maria Luisa
Cc: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
Many of the HCP experts are at OHBM, so replies might take longer.
I know from my own experience with HCP output to look here for the Freesurfer
subject directories:
subject-id/T1w/subject-id/label/*
subject-id/T1w/subject-id/mri/*
subject-id/T1w/subject-id/sur
Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
Hi Maria,
My bet is that the error you are seeing is coming from the last call to
recon-all in the FreeSurferPipeline.sh script. This would be in the
statements that look like:
#Final Recon-all Steps
log_Msg "Final Recon-all Steps"
recon-all -subjid $SubjectID -sd $SubjectDIR -surfvolume -parcstats
-cortparc2 -parcstats2 -cortparc3 -parcstats3 -cortribbon -segstats
-aparc2aseg -wmparc -balabels -label-exvivo-ec -openmp ${num_cores}
${seed_cmd_appendix}
log_Msg "Completed"
In particular, it would be the line that is shown in red above. (Note,
depending on the version of the HCP Pipelines you are using, your
version of the recon-all command may not have the -openmp ${num_cores}
or the ${seed_cmd_appendix} in it.)
The -balabels option is asking the recon-all command to "Create Brodmann
area labels by mapping from fsaverage".
You probably won't have an fsaverage directory in the subject directory
which you are processing (in your case the
/HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w directory). In
that case, recon-all creates one for you as a symbolic link to the
$FREESURFER_HOME/subjects/fsaverage directory.
It is in a subdirectory of that created fsaverage directory that files
like lh.BA1.label should be found.
So, the first things that needs to be determined in your case are:
* At the time of this failure, does the
/HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w/fsaverage
directory exist at all?
* If it does exist, is it a symbolic link to somewhere in your
FreeSurfer installation? (I believe it should be a link to the
${FREESURFER_HOME}/subjects/fsaverage directory.)
* What is the value of your FREESURFER_HOME environment variable?
Can you check into those things and let me know what you find?
Best Regards,
Tim
On 06/28/2017 09:41 AM, Mandelli, Maria Luisa wrote:
Hi!I installed the freesurfer-hcp and I got an error in the Freesurfer
pipeline here...in the label directory I dont see the file that the
script is looking for! (lh.BA1.label)
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
/usr/local/freesurfer/bin/recon-all
PWD
/HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w/hcp350014/label
CMD mri_label2label --srcsubject fsaverage --srclabel
/HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w/fsaverage/label/lh.BA1.label
--trgsubject hcp350014 --trglabel ./lh.BA1.label --hemi lh --regmethod
surface
*/Maria Luisa Mandelli, PhD/*
/Assistant Professional Researcher/
*University of California, San Francisco*
675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158
Language Neurobiology Lab
http://albalab.ucsf.edu/
Memory and Aging Center**
_http://memory.ucsf.edu/_
UCSF Dyslexia Center
http://dyslexia.ucsf.edu/
*From:* hcp-users-boun...@humanconnectome.org
on behalf of Mandelli, Maria
Luisa
*Sent:* Monday, June 26, 2017 1:52:02 PM
*To:* Dierker, Donna
*Cc:* hcp-users@humanconnectome.org
*Subject:* Re: [HCP-Users] pipeline structural PostFreesurfer wmparc
not found
thank you very much!I have the standard Freesurfer version!
I m going to try to the HCP one now!
*/Maria Luisa Mandelli, PhD/*
/Assistant Professional Researcher/
*University of California, San Francisco*
675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158
Language Neurobiology Lab
http://albalab.ucsf.edu/
Memory and Aging Center**
_http://memory.ucsf.edu/_
UCSF Dyslexia Center
http://dyslexia.ucsf.edu/
*From:* Dierker, Donna
*Sent:* Monday, June 26, 2017 11:54:40 AM
*To:* Mandelli, Maria Luisa
*Cc:* hcp-users@humanconnectome.org
*Subject:* Re: [HCP-Users] pipeline structural PostFreesurfer wmparc
not found
Many of the HCP experts are at OHBM, so replies might take longer.
I know from my own experience with HCP output to look here for the
Freesurfer subject directories:
subject-id/T1w/subject-id/label/*
subject-id/T1w/subject-id/mri/*
subject-id/T1w/subject-id/surf/*
…
Also see page 21 here:
http://humanconnectome.org/storage/app/media/documentation/s1200/HCP_S1200_Release_Appendix_III.pdf
Hopefully there is no problem! :)
But I must point out that there is a difference between the Freesurfer
v5.3 distribution and Freesurfer 5.3-HCP.
The latter uses both T1w & T2w images, which makes a big difference
(e.g., for myelin maps).
Not sure which you used, but it is an important difference.
> On Jun 26, 2017, at 12:27 PM, Mandelli, Maria Luisa
wrote:
>
> Hi!
> I m running the structural HCP pipeline and I m using Freesurfer v5.3
> It seems that the job finished without errors but I dont see the
files in the T1w folder of the subject.
> For example the wmparc_1mm files
> I m not sure where is the problem!
> Thank you
>
>
> Maria Luisa Mandelli, P
Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
Hi!I installed the freesurfer-hcp and I got an error in the Freesurfer pipeline here...in the label directory I dont see the file that the script is looking for! (lh.BA1.label) $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ /usr/local/freesurfer/bin/recon-all PWD /HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w/hcp350014/label CMD mri_label2label --srcsubject fsaverage --srclabel /HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w/fsaverage/label/lh.BA1.label --trgsubject hcp350014 --trglabel ./lh.BA1.label --hemi lh --regmethod surface Maria Luisa Mandelli, PhD Assistant Professional Researcher University of California, San Francisco 675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158 Language Neurobiology Lab http://albalab.ucsf.edu/ Memory and Aging Center http://memory.ucsf.edu/ UCSF Dyslexia Center http://dyslexia.ucsf.edu/ From: hcp-users-boun...@humanconnectome.org on behalf of Mandelli, Maria Luisa Sent: Monday, June 26, 2017 1:52:02 PM To: Dierker, Donna Cc: hcp-users@humanconnectome.org Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found thank you very much!I have the standard Freesurfer version! I m going to try to the HCP one now! Maria Luisa Mandelli, PhD Assistant Professional Researcher University of California, San Francisco 675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158 Language Neurobiology Lab http://albalab.ucsf.edu/ Memory and Aging Center http://memory.ucsf.edu/ UCSF Dyslexia Center http://dyslexia.ucsf.edu/ From: Dierker, Donna Sent: Monday, June 26, 2017 11:54:40 AM To: Mandelli, Maria Luisa Cc: hcp-users@humanconnectome.org Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found Many of the HCP experts are at OHBM, so replies might take longer. I know from my own experience with HCP output to look here for the Freesurfer subject directories: subject-id/T1w/subject-id/label/* subject-id/T1w/subject-id/mri/* subject-id/T1w/subject-id/surf/* … Also see page 21 here: http://humanconnectome.org/storage/app/media/documentation/s1200/HCP_S1200_Release_Appendix_III.pdf Hopefully there is no problem! :) But I must point out that there is a difference between the Freesurfer v5.3 distribution and Freesurfer 5.3-HCP. The latter uses both T1w & T2w images, which makes a big difference (e.g., for myelin maps). Not sure which you used, but it is an important difference. > On Jun 26, 2017, at 12:27 PM, Mandelli, Maria Luisa > wrote: > > Hi! > I m running the structural HCP pipeline and I m using Freesurfer v5.3 > It seems that the job finished without errors but I dont see the files in the > T1w folder of the subject. > For example the wmparc_1mm files > I m not sure where is the problem! > Thank you > > > Maria Luisa Mandelli, PhD > Assistant Professional Researcher > > University of California, San Francisco > 675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158 > > Language Neurobiology Lab > http://albalab.ucsf.edu/ > Memory and Aging Center > http://memory.ucsf.edu/ > UCSF Dyslexia Center > http://dyslexia.ucsf.edu/ > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
thank you very much!I have the standard Freesurfer version! I m going to try to the HCP one now! Maria Luisa Mandelli, PhD Assistant Professional Researcher University of California, San Francisco 675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158 Language Neurobiology Lab http://albalab.ucsf.edu/ Memory and Aging Center http://memory.ucsf.edu/ UCSF Dyslexia Center http://dyslexia.ucsf.edu/ From: Dierker, Donna Sent: Monday, June 26, 2017 11:54:40 AM To: Mandelli, Maria Luisa Cc: hcp-users@humanconnectome.org Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found Many of the HCP experts are at OHBM, so replies might take longer. I know from my own experience with HCP output to look here for the Freesurfer subject directories: subject-id/T1w/subject-id/label/* subject-id/T1w/subject-id/mri/* subject-id/T1w/subject-id/surf/* … Also see page 21 here: http://humanconnectome.org/storage/app/media/documentation/s1200/HCP_S1200_Release_Appendix_III.pdf Hopefully there is no problem! :) But I must point out that there is a difference between the Freesurfer v5.3 distribution and Freesurfer 5.3-HCP. The latter uses both T1w & T2w images, which makes a big difference (e.g., for myelin maps). Not sure which you used, but it is an important difference. > On Jun 26, 2017, at 12:27 PM, Mandelli, Maria Luisa > wrote: > > Hi! > I m running the structural HCP pipeline and I m using Freesurfer v5.3 > It seems that the job finished without errors but I dont see the files in the > T1w folder of the subject. > For example the wmparc_1mm files > I m not sure where is the problem! > Thank you > > > Maria Luisa Mandelli, PhD > Assistant Professional Researcher > > University of California, San Francisco > 675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158 > > Language Neurobiology Lab > http://albalab.ucsf.edu/ > Memory and Aging Center > http://memory.ucsf.edu/ > UCSF Dyslexia Center > http://dyslexia.ucsf.edu/ > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
Many of the HCP experts are at OHBM, so replies might take longer. I know from my own experience with HCP output to look here for the Freesurfer subject directories: subject-id/T1w/subject-id/label/* subject-id/T1w/subject-id/mri/* subject-id/T1w/subject-id/surf/* … Also see page 21 here: http://humanconnectome.org/storage/app/media/documentation/s1200/HCP_S1200_Release_Appendix_III.pdf Hopefully there is no problem! :) But I must point out that there is a difference between the Freesurfer v5.3 distribution and Freesurfer 5.3-HCP. The latter uses both T1w & T2w images, which makes a big difference (e.g., for myelin maps). Not sure which you used, but it is an important difference. > On Jun 26, 2017, at 12:27 PM, Mandelli, Maria Luisa > wrote: > > Hi! > I m running the structural HCP pipeline and I m using Freesurfer v5.3 > It seems that the job finished without errors but I dont see the files in the > T1w folder of the subject. > For example the wmparc_1mm files > I m not sure where is the problem! > Thank you > > > Maria Luisa Mandelli, PhD > Assistant Professional Researcher > > University of California, San Francisco > 675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158 > > Language Neurobiology Lab > http://albalab.ucsf.edu/ > Memory and Aging Center > http://memory.ucsf.edu/ > UCSF Dyslexia Center > http://dyslexia.ucsf.edu/ > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] pipeline structural PostFreesurfer wmparc not found
Hi! I m running the structural HCP pipeline and I m using Freesurfer v5.3 It seems that the job finished without errors but I dont see the files in the T1w folder of the subject. For example the wmparc_1mm files I m not sure where is the problem! Thank you Maria Luisa Mandelli, PhD Assistant Professional Researcher University of California, San Francisco 675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158 Language Neurobiology Lab http://albalab.ucsf.edu/ Memory and Aging Center http://memory.ucsf.edu/ UCSF Dyslexia Center http://dyslexia.ucsf.edu/ ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
