Re: [Freesurfer] isxconcat-sess error: trgsubject
isxconcat-sess assumes that you sampled all your subjects to the common surface (fsaverage). You will have to re-run selxavg3-sess using data on fsaverage. On 3/19/18 12:15 PM, Yagmur Ozdemir 19 wrote: Thank you for the help! root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim Sess01/bold/rtopyTR2.lh//mask.nii.gz 128461 1 1 1 root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim Sess02/bold/rtopyTR2.lh//mask.nii.gz 143033 1 1 1 root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim Sess03/bold/rtopyTR2.lh//mask.nii.gz 163154 1 1 1 root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim Sess04/bold/rtopyTR2.lh//mask.nii.gz 124330 1 1 1 root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim Sess07/bold/rtopyTR2.lh//mask.nii.gz 120332 1 1 1 root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim Sess08/bold/rtopyTR2.lh//mask.nii.gz 102780 1 1 1 root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim Sess09/bold/rtopyTR2.lh//mask.nii.gz 130063 1 1 1 root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim Sess10/bold/rtopyTR2.lh//mask.nii.gz 129873 1 1 1 *From:* freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [dgr...@mgh.harvard.edu] *Sent:* Monday, March 19, 2018 5:40 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] isxconcat-sess error: trgsubject Can you run mri_info --dim Sess01/bold/rtopyTR2.lh//mask.nii.gz for each of your subjects and send us the result? On 3/19/18 7:52 AM, Yagmur Ozdemir 19 wrote: Hello Freesurfer developers, I am trying to concatenate session files of different subjects using isxconcat-sess. I am not really sure why " INFO:trgsubject is self, this will fail unless all sessions are the same subject" pops up as I understand this is what isxconcat-sess is meant to do, and I used --subject fsaverage in some tries. I am not sure if there is something I am doing wrong, or the problem is coming from the "//" in the output lines. When I took out either Sess01 and Sess02 from the list to be sure it wasn't a problem specific to it, I got the same error. Below is the error output. Best Idil INFO: trgsubject is self, this will fail unless all sessions are the same subject group/rtopyTR2.lh/log/isxconcat.log cd /home/vm01/local/freesurfer/Project_bold isxconcat0-sess -f sessid -m mask -o group/rtopyTR2.lh/masks.nii.gz -a rtopyTR2.lh /home/vm01/local/freesurfer/Project_bold mri_concat /home/vm01/local/freesurfer/Project_bold/Sess01/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess02/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess03/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess04/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess07/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess08/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess09/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess10/bold/rtopyTR2.lh//mask.nii.gz --o group/rtopyTR2.lh/masks.nii.gz ninputs = 8 Checking inputs ERROR: dimension mismatch between /home/vm01/local/freesurfer/Project_bold/Sess01/bold/rtopyTR2.lh//mask.nii.gz and /home/vm01/local/freesurfer/Project_bold/Sess02/bold/rtopyTR2.lh//mask.nii.gz ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] isxconcat-sess error: trgsubject
Thank you! Best Idil From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [dgr...@mgh.harvard.edu] Sent: Monday, March 19, 2018 6:25 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] isxconcat-sess error: trgsubject isxconcat-sess assumes that you sampled all your subjects to the common surface (fsaverage). You will have to re-run selxavg3-sess using data on fsaverage. On 3/19/18 12:15 PM, Yagmur Ozdemir 19 wrote: Thank you for the help! root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim Sess01/bold/rtopyTR2.lh//mask.nii.gz 128461 1 1 1 root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim Sess02/bold/rtopyTR2.lh//mask.nii.gz 143033 1 1 1 root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim Sess03/bold/rtopyTR2.lh//mask.nii.gz 163154 1 1 1 root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim Sess04/bold/rtopyTR2.lh//mask.nii.gz 124330 1 1 1 root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim Sess07/bold/rtopyTR2.lh//mask.nii.gz 120332 1 1 1 root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim Sess08/bold/rtopyTR2.lh//mask.nii.gz 102780 1 1 1 root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim Sess09/bold/rtopyTR2.lh//mask.nii.gz 130063 1 1 1 root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim Sess10/bold/rtopyTR2.lh//mask.nii.gz 129873 1 1 1 From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Douglas Greve [dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>] Sent: Monday, March 19, 2018 5:40 PM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] isxconcat-sess error: trgsubject Can you run mri_info --dim Sess01/bold/rtopyTR2.lh//mask.nii.gz for each of your subjects and send us the result? On 3/19/18 7:52 AM, Yagmur Ozdemir 19 wrote: Hello Freesurfer developers, I am trying to concatenate session files of different subjects using isxconcat-sess. I am not really sure why " INFO:trgsubject is self, this will fail unless all sessions are the same subject" pops up as I understand this is what isxconcat-sess is meant to do, and I used --subject fsaverage in some tries. I am not sure if there is something I am doing wrong, or the problem is coming from the "//" in the output lines. When I took out either Sess01 and Sess02 from the list to be sure it wasn't a problem specific to it, I got the same error. Below is the error output. Best Idil INFO: trgsubject is self, this will fail unless all sessions are the same subject group/rtopyTR2.lh/log/isxconcat.log cd /home/vm01/local/freesurfer/Project_bold isxconcat0-sess -f sessid -m mask -o group/rtopyTR2.lh/masks.nii.gz -a rtopyTR2.lh /home/vm01/local/freesurfer/Project_bold mri_concat /home/vm01/local/freesurfer/Project_bold/Sess01/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess02/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess03/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess04/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess07/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess08/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess09/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess10/bold/rtopyTR2.lh//mask.nii.gz --o group/rtopyTR2.lh/masks.nii.gz ninputs = 8 Checking inputs ERROR: dimension mismatch between /home/vm01/local/freesurfer/Project_bold/Sess01/bold/rtopyTR2.lh//mask.nii.gz and /home/vm01/local/freesurfer/Project_bold/Sess02/bold/rtopyTR2.lh//mask.nii.gz ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] isxconcat-sess error: trgsubject
Thank you for the help! root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim Sess01/bold/rtopyTR2.lh//mask.nii.gz 128461 1 1 1 root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim Sess02/bold/rtopyTR2.lh//mask.nii.gz 143033 1 1 1 root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim Sess03/bold/rtopyTR2.lh//mask.nii.gz 163154 1 1 1 root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim Sess04/bold/rtopyTR2.lh//mask.nii.gz 124330 1 1 1 root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim Sess07/bold/rtopyTR2.lh//mask.nii.gz 120332 1 1 1 root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim Sess08/bold/rtopyTR2.lh//mask.nii.gz 102780 1 1 1 root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim Sess09/bold/rtopyTR2.lh//mask.nii.gz 130063 1 1 1 root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim Sess10/bold/rtopyTR2.lh//mask.nii.gz 129873 1 1 1 From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [dgr...@mgh.harvard.edu] Sent: Monday, March 19, 2018 5:40 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] isxconcat-sess error: trgsubject Can you run mri_info --dim Sess01/bold/rtopyTR2.lh//mask.nii.gz for each of your subjects and send us the result? On 3/19/18 7:52 AM, Yagmur Ozdemir 19 wrote: Hello Freesurfer developers, I am trying to concatenate session files of different subjects using isxconcat-sess. I am not really sure why " INFO:trgsubject is self, this will fail unless all sessions are the same subject" pops up as I understand this is what isxconcat-sess is meant to do, and I used --subject fsaverage in some tries. I am not sure if there is something I am doing wrong, or the problem is coming from the "//" in the output lines. When I took out either Sess01 and Sess02 from the list to be sure it wasn't a problem specific to it, I got the same error. Below is the error output. Best Idil INFO: trgsubject is self, this will fail unless all sessions are the same subject group/rtopyTR2.lh/log/isxconcat.log cd /home/vm01/local/freesurfer/Project_bold isxconcat0-sess -f sessid -m mask -o group/rtopyTR2.lh/masks.nii.gz -a rtopyTR2.lh /home/vm01/local/freesurfer/Project_bold mri_concat /home/vm01/local/freesurfer/Project_bold/Sess01/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess02/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess03/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess04/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess07/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess08/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess09/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess10/bold/rtopyTR2.lh//mask.nii.gz --o group/rtopyTR2.lh/masks.nii.gz ninputs = 8 Checking inputs ERROR: dimension mismatch between /home/vm01/local/freesurfer/Project_bold/Sess01/bold/rtopyTR2.lh//mask.nii.gz and /home/vm01/local/freesurfer/Project_bold/Sess02/bold/rtopyTR2.lh//mask.nii.gz ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] isxconcat-sess error: trgsubject
Can you run mri_info --dim Sess01/bold/rtopyTR2.lh//mask.nii.gz for each of your subjects and send us the result? On 3/19/18 7:52 AM, Yagmur Ozdemir 19 wrote: Hello Freesurfer developers, I am trying to concatenate session files of different subjects using isxconcat-sess. I am not really sure why " INFO:trgsubject is self, this will fail unless all sessions are the same subject" pops up as I understand this is what isxconcat-sess is meant to do, and I used --subject fsaverage in some tries. I am not sure if there is something I am doing wrong, or the problem is coming from the "//" in the output lines. When I took out either Sess01 and Sess02 from the list to be sure it wasn't a problem specific to it, I got the same error. Below is the error output. Best Idil INFO: trgsubject is self, this will fail unless all sessions are the same subject group/rtopyTR2.lh/log/isxconcat.log cd /home/vm01/local/freesurfer/Project_bold isxconcat0-sess -f sessid -m mask -o group/rtopyTR2.lh/masks.nii.gz -a rtopyTR2.lh /home/vm01/local/freesurfer/Project_bold mri_concat /home/vm01/local/freesurfer/Project_bold/Sess01/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess02/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess03/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess04/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess07/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess08/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess09/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess10/bold/rtopyTR2.lh//mask.nii.gz --o group/rtopyTR2.lh/masks.nii.gz ninputs = 8 Checking inputs ERROR: dimension mismatch between /home/vm01/local/freesurfer/Project_bold/Sess01/bold/rtopyTR2.lh//mask.nii.gz and /home/vm01/local/freesurfer/Project_bold/Sess02/bold/rtopyTR2.lh//mask.nii.gz ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] isxconcat-sess error: trgsubject
Hello Freesurfer developers, I am trying to concatenate session files of different subjects using isxconcat-sess. I am not really sure why " INFO:trgsubject is self, this will fail unless all sessions are the same subject" pops up as I understand this is what isxconcat-sess is meant to do, and I used --subject fsaverage in some tries. I am not sure if there is something I am doing wrong, or the problem is coming from the "//" in the output lines. When I took out either Sess01 and Sess02 from the list to be sure it wasn't a problem specific to it, I got the same error. Below is the error output. Best Idil INFO: trgsubject is self, this will fail unless all sessions are the same subject group/rtopyTR2.lh/log/isxconcat.log cd /home/vm01/local/freesurfer/Project_bold isxconcat0-sess -f sessid -m mask -o group/rtopyTR2.lh/masks.nii.gz -a rtopyTR2.lh /home/vm01/local/freesurfer/Project_bold mri_concat /home/vm01/local/freesurfer/Project_bold/Sess01/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess02/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess03/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess04/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess07/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess08/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess09/bold/rtopyTR2.lh//mask.nii.gz /home/vm01/local/freesurfer/Project_bold/Sess10/bold/rtopyTR2.lh//mask.nii.gz --o group/rtopyTR2.lh/masks.nii.gz ninputs = 8 Checking inputs ERROR: dimension mismatch between /home/vm01/local/freesurfer/Project_bold/Sess01/bold/rtopyTR2.lh//mask.nii.gz and /home/vm01/local/freesurfer/Project_bold/Sess02/bold/rtopyTR2.lh//mask.nii.gz ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Isxconcat-sess error
Hi Freesurfer experts, I'm trying to concatenate subjects using the command isxconcat-sess -d $SUBJECTS_DIR -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/TEST -analysis SIRP_LoadRegression_Stable5_072915 -c Cond2vFix -hemis -o /cluster/roffman/users/STable5_PerRun/Analyses_GDD/GDD_All/100_GDD_92Adults_8Adolescents/TEST I'm receiving the error ERROR: cannot find /autofs/cluster/roffman/users/Stable5_PerRun/GDDA147/bold/register.dof6.dat I have register.dof6.dat in my run folders, but not in the general bold folder. I know that I can create a register.dof6.dat file in my bold folder if I run registration on my subjects -per-session. However, I want my subjects to stay preprocessed and registered -per-run. The analysis used in the isxconcat-sess command is also specified to be -per-run. The command I used to make it was mkanalysis-sess -analysis SIRP_LoadRegression_Stable5_072915 -TR 2 -paradigm slopepar -event-related -fsd bold -runlistfile runlistfile -tpef tpef_1.5mm.txt -native -timewindow 20 -TER 2 -nconditions 9 -gammafit 2.25 1.25 -refeventdur 2 -fwhm 5 -per-run Is there a way to specify in the concatenation command that my subjects are registered -per-run, and that the command should not look in the bold folder for the register.dof6.dat file, but instead in the run folders? Thanks, Anais ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] isxconcat-sess
Hi Surfers and Doug, I was trying to average two scan sessions of the same subject and isxconcat-sess under dev-env failed again. This time I get this message: ERROR: cannot find /autofs/cluster/tootell/pitcairn/1/shahin/FeatureAttention_Color/Subjects2/hron1/bold/Attention_TR3_FHWM0_PR_Ver2.lh/nmask.dat Which is true! this file does not exist. Regards On Thu, May 14, 2015 at 10:39 PM, SHAHIN NASR sha...@nmr.mgh.harvard.edu wrote: Hi Doug, It works without any error. Thanks a lot On Thu, May 14, 2015 at 5:47 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: I just made a fix. Can you try it out and let me know if it works? On 05/14/2015 11:38 AM, SHAHIN NASR wrote: Hi, Does anyone know what has changed in isxconcat-sess command in nmr-dev-env? Previously I could use it to average different sessions of the same subject. But now I am getting this error: INFO: trgsubject is self, this will fail unless all sessions are the same subject ERROR: cannot find /cluster/tootell/pitcairn/1/users/good_subjects_anat//self/mri.2mm/subcort.mask.mgz Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] isxconcat-sess
Hi, Does anyone know what has changed in isxconcat-sess command in nmr-dev-env? Previously I could use it to average different sessions of the same subject. But now I am getting this error: INFO: trgsubject is self, this will fail unless all sessions are the same subject ERROR: cannot find /cluster/tootell/pitcairn/1/users/good_subjects_anat//self/mri.2mm/subcort.mask.mgz Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] isxconcat-sess
I just made a fix. Can you try it out and let me know if it works? On 05/14/2015 11:38 AM, SHAHIN NASR wrote: Hi, Does anyone know what has changed in isxconcat-sess command in nmr-dev-env? Previously I could use it to average different sessions of the same subject. But now I am getting this error: INFO: trgsubject is self, this will fail unless all sessions are the same subject ERROR: cannot find /cluster/tootell/pitcairn/1/users/good_subjects_anat//self/mri.2mm/subcort.mask.mgz Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] isxconcat-sess
Hi Doug, It works without any error. Thanks a lot On Thu, May 14, 2015 at 5:47 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: I just made a fix. Can you try it out and let me know if it works? On 05/14/2015 11:38 AM, SHAHIN NASR wrote: Hi, Does anyone know what has changed in isxconcat-sess command in nmr-dev-env? Previously I could use it to average different sessions of the same subject. But now I am getting this error: INFO: trgsubject is self, this will fail unless all sessions are the same subject ERROR: cannot find /cluster/tootell/pitcairn/1/users/good_subjects_anat//self/mri.2mm/subcort.mask.mgz Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] isxconcat-sess without fsaverage
I put it here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/isxconcat-sess If you just want to concatenate the vertex values, then just do something like mri_concat --o output.nii.gz sess1/bold/analysis/contrast/ces.nii.gz sess2/bold/analysis/contrast/ces.nii.gz ... On 04/27/2015 02:28 PM, Reza Rajimehr wrote: Thanks Doug! Could you put the updated isxconcat-sess script in an ftp server and provide a link so that I can download it? I do not have access to the dev environment. Now I should run the command with the flag -trgsubject F99, right? My analysis is on the surface, and I only want to concatenate the vertex values. I have an orig.mgz file in the mri subdirectory of F99, but I hope isxconcat-sess does not ask for additional volume files. Best, Reza I just fixed this for the dev environment. Try running it from there. Though I think this is just the start of the problems. doug On Monday, April 27, 2015, Reza Rajimehr rajim...@gmail.com mailto:rajim...@gmail.com wrote: Hi, I am trying to use isxconcat-sess for averaging functional data across two monkeys. The data in two monkeys have been analyzed on a common surface (F99). When I run this: isxconcat-sess -sf MonkeysList.txt -analysis movie2.task.rh -all-contrasts -o group2 I get an error: ERROR: cannot find /home/reza/Data/structurals//fsaverage/mri.2mm/subcort.mask.mgz Even when I add -trgsubject F99 to the command, I get the same error. How can I tell isxconcat-sess not to use fsaverage? I am using Freesurfer v5.3 stable. Thanks, Reza ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] isxconcat-sess without fsaverage
You can mri_concat the cesvar files. For the dof, just add up the dofs in each run. On 04/27/2015 05:08 PM, Reza Rajimehr wrote: If I use mri_concat instead of isxconcat-sess, will I have all the necessary files for fixed-effects averaging by mri_glmfit? Specifically, can I generate cesvar.nii for --yffxvar and ffxdof.dat for --ffxdofdat in mri_glmfit? Reza I put it here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/isxconcat-sess If you just want to concatenate the vertex values, then just do something like mri_concat --o output.nii.gz sess1/bold/analysis/contrast/ces.nii.gz sess2/bold/analysis/contrast/ces.nii.gz ... On Monday, April 27, 2015, Reza Rajimehr rajim...@gmail.com mailto:rajim...@gmail.com wrote: Thanks Doug! Could you put the updated isxconcat-sess script in an ftp server and provide a link so that I can download it? I do not have access to the dev environment. Now I should run the command with the flag -trgsubject F99, right? My analysis is on the surface, and I only want to concatenate the vertex values. I have an orig.mgz file in the mri subdirectory of F99, but I hope isxconcat-sess does not ask for additional volume files. Best, Reza I just fixed this for the dev environment. Try running it from there. Though I think this is just the start of the problems. doug On Monday, April 27, 2015, Reza Rajimehr rajim...@gmail.com javascript:_e(%7B%7D,'cvml','rajim...@gmail.com'); wrote: Hi, I am trying to use isxconcat-sess for averaging functional data across two monkeys. The data in two monkeys have been analyzed on a common surface (F99). When I run this: isxconcat-sess -sf MonkeysList.txt -analysis movie2.task.rh -all-contrasts -o group2 I get an error: ERROR: cannot find /home/reza/Data/structurals//fsaverage/mri.2mm/subcort.mask.mgz Even when I add -trgsubject F99 to the command, I get the same error. How can I tell isxconcat-sess not to use fsaverage? I am using Freesurfer v5.3 stable. Thanks, Reza ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] isxconcat-sess without fsaverage
If I use mri_concat instead of isxconcat-sess, will I have all the necessary files for fixed-effects averaging by mri_glmfit? Specifically, can I generate cesvar.nii for --yffxvar and ffxdof.dat for --ffxdofdat in mri_glmfit? Reza I put it here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/isxconcat-sess If you just want to concatenate the vertex values, then just do something like mri_concat --o output.nii.gz sess1/bold/analysis/contrast/ces.nii.gz sess2/bold/analysis/contrast/ces.nii.gz ... On Monday, April 27, 2015, Reza Rajimehr rajim...@gmail.com wrote: Thanks Doug! Could you put the updated isxconcat-sess script in an ftp server and provide a link so that I can download it? I do not have access to the dev environment. Now I should run the command with the flag -trgsubject F99, right? My analysis is on the surface, and I only want to concatenate the vertex values. I have an orig.mgz file in the mri subdirectory of F99, but I hope isxconcat-sess does not ask for additional volume files. Best, Reza I just fixed this for the dev environment. Try running it from there. Though I think this is just the start of the problems. doug On Monday, April 27, 2015, Reza Rajimehr rajim...@gmail.com javascript:_e(%7B%7D,'cvml','rajim...@gmail.com'); wrote: Hi, I am trying to use isxconcat-sess for averaging functional data across two monkeys. The data in two monkeys have been analyzed on a common surface (F99). When I run this: isxconcat-sess -sf MonkeysList.txt -analysis movie2.task.rh -all-contrasts -o group2 I get an error: ERROR: cannot find /home/reza/Data/structurals//fsaverage/mri.2mm/subcort.mask.mgz Even when I add -trgsubject F99 to the command, I get the same error. How can I tell isxconcat-sess not to use fsaverage? I am using Freesurfer v5.3 stable. Thanks, Reza ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] isxconcat-sess without fsaverage
Thanks Doug! Could you clarify a bit more on how to add up the dofs in each run? You can mri_concat the cesvar files. For the dof, just add up the dofs in each run. On Monday, April 27, 2015, Reza Rajimehr rajim...@gmail.com wrote: If I use mri_concat instead of isxconcat-sess, will I have all the necessary files for fixed-effects averaging by mri_glmfit? Specifically, can I generate cesvar.nii for --yffxvar and ffxdof.dat for --ffxdofdat in mri_glmfit? Reza I put it here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/isxconcat-sess If you just want to concatenate the vertex values, then just do something like mri_concat --o output.nii.gz sess1/bold/analysis/contrast/ces.nii.gz sess2/bold/analysis/contrast/ces.nii.gz ... On Monday, April 27, 2015, Reza Rajimehr rajim...@gmail.com javascript:_e(%7B%7D,'cvml','rajim...@gmail.com'); wrote: Thanks Doug! Could you put the updated isxconcat-sess script in an ftp server and provide a link so that I can download it? I do not have access to the dev environment. Now I should run the command with the flag -trgsubject F99, right? My analysis is on the surface, and I only want to concatenate the vertex values. I have an orig.mgz file in the mri subdirectory of F99, but I hope isxconcat-sess does not ask for additional volume files. Best, Reza I just fixed this for the dev environment. Try running it from there. Though I think this is just the start of the problems. doug On Monday, April 27, 2015, Reza Rajimehr rajim...@gmail.com wrote: Hi, I am trying to use isxconcat-sess for averaging functional data across two monkeys. The data in two monkeys have been analyzed on a common surface (F99). When I run this: isxconcat-sess -sf MonkeysList.txt -analysis movie2.task.rh -all-contrasts -o group2 I get an error: ERROR: cannot find /home/reza/Data/structurals//fsaverage/mri.2mm/subcort.mask.mgz Even when I add -trgsubject F99 to the command, I get the same error. How can I tell isxconcat-sess not to use fsaverage? I am using Freesurfer v5.3 stable. Thanks, Reza ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] isxconcat-sess without fsaverage
Eachoutput.nii.gz sess1/bold/analysis folder will have a dof.dat file with a number in it. Add up all those numbers, create a files with the sum in it, and pass that file to mrI_gomfit. On 04/27/2015 06:18 PM, Reza Rajimehr wrote: Thanks Doug! Could you clarify a bit more on how to add up the dofs in each run? You can mri_concat the cesvar files. For the dof, just add up the dofs in each run. On Monday, April 27, 2015, Reza Rajimehr rajim...@gmail.com mailto:rajim...@gmail.com wrote: If I use mri_concat instead of isxconcat-sess, will I have all the necessary files for fixed-effects averaging by mri_glmfit? Specifically, can I generate cesvar.nii for --yffxvar and ffxdof.dat for --ffxdofdat in mri_glmfit? Reza I put it here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/isxconcat-sess If you just want to concatenate the vertex values, then just do something like mri_concat --o output.nii.gz sess1/bold/analysis/contrast/ces.nii.gz sess2/bold/analysis/contrast/ces.nii.gz ... On Monday, April 27, 2015, Reza Rajimehr rajim...@gmail.com javascript:_e(%7B%7D,'cvml','rajim...@gmail.com'); wrote: Thanks Doug! Could you put the updated isxconcat-sess script in an ftp server and provide a link so that I can download it? I do not have access to the dev environment. Now I should run the command with the flag -trgsubject F99, right? My analysis is on the surface, and I only want to concatenate the vertex values. I have an orig.mgz file in the mri subdirectory of F99, but I hope isxconcat-sess does not ask for additional volume files. Best, Reza I just fixed this for the dev environment. Try running it from there. Though I think this is just the start of the problems. doug On Monday, April 27, 2015, Reza Rajimehr rajim...@gmail.com wrote: Hi, I am trying to use isxconcat-sess for averaging functional data across two monkeys. The data in two monkeys have been analyzed on a common surface (F99). When I run this: isxconcat-sess -sf MonkeysList.txt -analysis movie2.task.rh -all-contrasts -o group2 I get an error: ERROR: cannot find /home/reza/Data/structurals//fsaverage/mri.2mm/subcort.mask.mgz Even when I add -trgsubject F99 to the command, I get the same error. How can I tell isxconcat-sess not to use fsaverage? I am using Freesurfer v5.3 stable. Thanks, Reza ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] isxconcat-sess without fsaverage
Thanks Doug! Could you put the updated isxconcat-sess script in an ftp server and provide a link so that I can download it? I do not have access to the dev environment. Now I should run the command with the flag -trgsubject F99, right? My analysis is on the surface, and I only want to concatenate the vertex values. I have an orig.mgz file in the mri subdirectory of F99, but I hope isxconcat-sess does not ask for additional volume files. Best, Reza I just fixed this for the dev environment. Try running it from there. Though I think this is just the start of the problems. doug On Monday, April 27, 2015, Reza Rajimehr rajim...@gmail.com wrote: Hi, I am trying to use isxconcat-sess for averaging functional data across two monkeys. The data in two monkeys have been analyzed on a common surface (F99). When I run this: isxconcat-sess -sf MonkeysList.txt -analysis movie2.task.rh -all-contrasts -o group2 I get an error: ERROR: cannot find /home/reza/Data/structurals//fsaverage/mri.2mm/subcort.mask.mgz Even when I add -trgsubject F99 to the command, I get the same error. How can I tell isxconcat-sess not to use fsaverage? I am using Freesurfer v5.3 stable. Thanks, Reza ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] isxconcat-sess without fsaverage
Hi, I am trying to use isxconcat-sess for averaging functional data across two monkeys. The data in two monkeys have been analyzed on a common surface (F99). When I run this: isxconcat-sess -sf MonkeysList.txt -analysis movie2.task.rh -all-contrasts -o group2 I get an error: ERROR: cannot find /home/reza/Data/structurals//fsaverage/mri.2mm/subcort.mask.mgz Even when I add -trgsubject F99 to the command, I get the same error. How can I tell isxconcat-sess not to use fsaverage? I am using Freesurfer v5.3 stable. Thanks, Reza ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] isxconcat-sess problem
Hi list, I'm performing the FS-FAST analysis. Some months ago, I have already preformed this analysis on some subjects without problem. Now, I have added some subjects. When I rerun the analysis i have these error: for isxconcat-sess -sf sessidlist —analysis fc.lthalseed.surf.lh -contrast L_Thalamus -o my-group_thal_LHERROR: finding sessionsSess47 /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess15 /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess48 /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess49 /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess50[iMac-di-Stefano:freesurfer/subjects/FUNCTIONAL_DATA] Stefano% and for isxconcat-sess -s Sess01 -s Sess02 -s Sess03 -s Sess04 -s Sess05 -s Sess06 -s Sess07 -s Sess08 -s Sess09 -s Sess10 -s Sess11 -s Sess12 -s Sess13 —s Sess14 -s Sess15 -s Sess16 -s Sess30 -s Sess31 -s Sess32 -s Sess33 -s Sess34 -s Sess35 -s Sess36 -s Sess37 -s Sess39 -s Sess40 -s Sess41 -s Sess42 -s Sess43 -s Sess44 -s Sess45 -s Sess46 -s Sess47 -s Sess48 —s Sess49 -s Sess50 —analysis fc.lthalseed.surf.lh -contrast L_Thalamus -o my-group_THAL_LEFTERROR: Flag —s unrecognized. FUNCTIONAL_DATA directory contains: file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/fc.lamgseed.surf.lh/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/fc.lthalseed.surf.lh/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/fc.ramgseed.surf.rh/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/fc.rthalseed.surf.rh/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/file.fsgdfile:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/g1g2.intercept.mtxfile:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/group.diff.mtxfile:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/group1.mtxfile:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/group2.mtxfile:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/GroupDescriptorFile%201file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/log/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/mean.L_Amygdala.configfile:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/mean.L_Thalamus.configfile:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/mean.R_Amygdala.configfile:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/mean.R_Thalamus.configfile:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess02/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess03/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess04/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess05/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess06/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess07/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess08/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess09/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess10/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess11/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess12/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess13/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess14/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess15/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess16/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess30/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess31/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess32/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess33/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess34/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess35/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess36/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess37/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess39/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess40/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess41/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess42/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess43/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess44/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess45/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess46/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess47/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess48/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess49/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess50/file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/sessidlist for each subject, i.e. within
Re: [Freesurfer] isxconcat-sess error in generating mni305.rho1mn
Hi NewFei, canyou run the following commands and send me dng.log ? cd /autofs/space/audrey_001/users/FSFASTFC isxconcat0-sess -m pcc -o matchedCTRLSCHIZ.rhDG.newest/noGMrhDGmc6/X/mni305.pcc.nii.gz -sf matchedCTRLSCHIZ.txt -d /autofs/space/audrey_001/users/FSFASTFC -c X -a noGMrhDGmc6 -split -interp trilin -reg register.dof6.dat -talres 2 | tee dng.log doug On 01/25/2013 11:49 AM, New Fei Ho wrote: Hi Doug, I've attached the isxconcat-sess log. I'm able to concatenate the subjects into one file, and generate the masks. I'm not able to obtain the rho values because the subject design matrix could not be sourced. $Id: isxconcat-sess,v 1.60 2011/03/10 15:58:15 greve Exp $ Fri Jan 25 11:04:10 EST 2013 Linux audrey 2.6.32-279.14.1.el6.x86_64 #1 SMP Tue Nov 6 23:43:09 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux /autofs/space/audrey_001/users/FSFASTFC /usr/local/freesurfer/stable5_1_0/fsfast/bin/isxconcat-sess -a noGMrhDGmc6 -sf matchedCTRLSCHIZ.txt -d /autofs/space/audrey_001/users/FSFASTFC -o matchedCTRLSCHIZ.rhDG.newest -all-contrasts -m pcc Do you know what went wrong? Thanks, Newfei -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] isxconcat-sess error in generating mni305.rho1mn
There's a bunch of stuff in the analysis folder (noGMrhDGmc6) including some .mat files. FSFAST sees these .mat files and thinks they are contrasts. So, you can remove all the extra stuff in that folder or you can spec the contrast with -contrast. doug On 01/25/2013 11:49 AM, New Fei Ho wrote: Hi Doug, I've attached the isxconcat-sess log. I'm able to concatenate the subjects into one file, and generate the masks. I'm not able to obtain the rho values because the subject design matrix could not be sourced. $Id: isxconcat-sess,v 1.60 2011/03/10 15:58:15 greve Exp $ Fri Jan 25 11:04:10 EST 2013 Linux audrey 2.6.32-279.14.1.el6.x86_64 #1 SMP Tue Nov 6 23:43:09 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux /autofs/space/audrey_001/users/FSFASTFC /usr/local/freesurfer/stable5_1_0/fsfast/bin/isxconcat-sess -a noGMrhDGmc6 -sf matchedCTRLSCHIZ.txt -d /autofs/space/audrey_001/users/FSFASTFC -o matchedCTRLSCHIZ.rhDG.newest -all-contrasts -m pcc Do you know what went wrong? Thanks, Newfei -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] isxconcat-sess missing dof file
It looks like that file is there now. Is the problem fixed? doug Chindhuri Selvadurai wrote: Hi all, When I run isxconcat-sess, I am experiencing an error finding a 'dof' file in my analysis directories within the FSD files. subjects directory: /cluster/manoach/milton/subjects command line: isxconcat-sess -sf sessid_all -analysis mstmct_v_base -c type_v_rest_vol -o /cluster/manoach/milton/subjects/group_analysis/volume/ output: /cluster/manoach/milton/subjects/group_analysis/volume//mstmct_v_base/log/isxconcat.log ERROR: cannot find /autofs/cluster/manoach/milton/subjects/PAMST02/bold/mstmct_v_base/dof Did I miss a step before the isxconcat? Thank you! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] isxconcat-sess missing dof file
Hi all, When I run isxconcat-sess, I am experiencing an error finding a 'dof' file in my analysis directories within the FSD files. subjects directory: /cluster/manoach/milton/subjects command line: isxconcat-sess -sf sessid_all -analysis mstmct_v_base -c type_v_rest_vol -o /cluster/manoach/milton/subjects/group_analysis/volume/ output: /cluster/manoach/milton/subjects/group_analysis/volume//mstmct_v_base/log/isxconcat.log ERROR: cannot find /autofs/cluster/manoach/milton/subjects/PAMST02/bold/mstmct_v_base/dof Did I miss a step before the isxconcat? Thank you! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] isxconcat-sess question..
Hi Krishna, if you have a proper freesurfer analysis and registration to the anatomical, it should work fine. doug Krishna Srihasam wrote: Hi, Is there a way to use” isxconcat-sess” to average monkey fMRI data? i.e. I have two groups of monkeys (say, test and control groups) and I want to do group analysis on their data.. Regards, krishna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] isxconcat-sess question
Hi, Is there a way to use” isxconcat-sess” to average monkey fMRI data? i.e. I have two groups of monkeys (say, test and control groups) and I want to do group analysis on their data.. Regards, krishna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] isxconcat-sess question..
Hi, Is there a way to use isxconcat-sess to average monkey fMRI data? i.e. I have two groups of monkeys (say, test and control groups) and I want to do group analysis on their data.. Regards, krishna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] isxconcat-sess
isxconcat-sess creates the files that you pass to mri_glmfit (ie, multi-frame volumes and/or surfaces where each frame is a subject). Something like: AVG08/Analyse_Simple_Confidence/High_confidence__Low_confidence_vs_HSF_gabor__LSF_gabor/tal.ces.nii You can then use this as input to mri_glmfit passing it with the --y option. You can get more help from the FS FAST tutorial. Go to the wiki, type isxconcat-sess in the Search field, then hit the Text button. doug On Wed, 14 Oct 2009, Maximilien Chaumon wrote: Hi freesurfers, I've been running isxconcat-sess with this line chaumon[/homes/11/chaumon/data] (nmr-std-env) isxconcat-sess -sf subjlist.txt -analysis Analyse_Simple_Confidence -c High_confidence__Low_confidence_vs_HSF_gabor__LSF_gabor -o AVG08 I was expecting to find a directory called osgm in the specified analysis directory with which I could feed data to mri_glmfit, but I can't find it. /homes/11/chaumon/bomba/AVG08/Analyse_Simple_Confidence/High_confidence__Low_confidence_vs_HSF_gabor__LSF_gabor The log file is attached. I don't find error in the text. Where am I wrong? Is there any mri_glmfit-sess like script somewhere? It's going to be pretty tough to find each parameter to feed to mri_glmfit... Thanks, Max -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] isxconcat-sess
Thanks Doug, I was just a bit confused because I thought the help for mri_glmfit mentioned an osgm directory that wasn't there. I was given a matlab script that does that now. I'm using a command like this: mri_glmfit --y tal.ces.000.nii --osgm --glmdir tal.rfx.osgm --nii --mask ../tal.mask.nii Thanks Mx 2009/10/15 Doug Greve gr...@nmr.mgh.harvard.edu isxconcat-sess creates the files that you pass to mri_glmfit (ie, multi-frame volumes and/or surfaces where each frame is a subject). Something like: AVG08/Analyse_Simple_Confidence/High_confidence__Low_confidence_vs_HSF_gabor__LSF_gabor/tal.ces.nii You can then use this as input to mri_glmfit passing it with the --y option. You can get more help from the FS FAST tutorial. Go to the wiki, type isxconcat-sess in the Search field, then hit the Text button. doug On Wed, 14 Oct 2009, Maximilien Chaumon wrote: Hi freesurfers, I've been running isxconcat-sess with this line chaumon[/homes/11/chaumon/data] (nmr-std-env) isxconcat-sess -sf subjlist.txt -analysis Analyse_Simple_Confidence -c High_confidence__Low_confidence_vs_HSF_gabor__LSF_gabor -o AVG08 I was expecting to find a directory called osgm in the specified analysis directory with which I could feed data to mri_glmfit, but I can't find it. /homes/11/chaumon/bomba/AVG08/Analyse_Simple_Confidence/High_confidence__Low_confidence_vs_HSF_gabor__LSF_gabor The log file is attached. I don't find error in the text. Where am I wrong? Is there any mri_glmfit-sess like script somewhere? It's going to be pretty tough to find each parameter to feed to mri_glmfit... Thanks, Max -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] isxconcat-sess
What does your matlab script do? Your glmfit cmd looks fine. On Thu, 15 Oct 2009, Maximilien Chaumon wrote: Thanks Doug, I was just a bit confused because I thought the help for mri_glmfit mentioned an osgm directory that wasn't there. I was given a matlab script that does that now. I'm using a command like this: mri_glmfit --y tal.ces.000.nii --osgm --glmdir tal.rfx.osgm --nii --mask ../tal.mask.nii Thanks Mx 2009/10/15 Doug Greve gr...@nmr.mgh.harvard.edu isxconcat-sess creates the files that you pass to mri_glmfit (ie, multi-frame volumes and/or surfaces where each frame is a subject). Something like: AVG08/Analyse_Simple_Confidence/High_confidence__Low_confidence_vs_HSF_gabor__LSF_gabor/tal.ces.nii You can then use this as input to mri_glmfit passing it with the --y option. You can get more help from the FS FAST tutorial. Go to the wiki, type isxconcat-sess in the Search field, then hit the Text button. doug On Wed, 14 Oct 2009, Maximilien Chaumon wrote: Hi freesurfers, I've been running isxconcat-sess with this line chaumon[/homes/11/chaumon/data] (nmr-std-env) isxconcat-sess -sf subjlist.txt -analysis Analyse_Simple_Confidence -c High_confidence__Low_confidence_vs_HSF_gabor__LSF_gabor -o AVG08 I was expecting to find a directory called osgm in the specified analysis directory with which I could feed data to mri_glmfit, but I can't find it. /homes/11/chaumon/bomba/AVG08/Analyse_Simple_Confidence/High_confidence__Low_confidence_vs_HSF_gabor__LSF_gabor The log file is attached. I don't find error in the text. Where am I wrong? Is there any mri_glmfit-sess like script somewhere? It's going to be pretty tough to find each parameter to feed to mri_glmfit... Thanks, Max -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] isxconcat-sess
Hi freesurfers, I've been running isxconcat-sess with this line chaumon[/homes/11/chaumon/data] (nmr-std-env) isxconcat-sess -sf subjlist.txt -analysis Analyse_Simple_Confidence -c High_confidence__Low_confidence_vs_HSF_gabor__LSF_gabor -o AVG08 I was expecting to find a directory called osgm in the specified analysis directory with which I could feed data to mri_glmfit, but I can't find it. /homes/11/chaumon/bomba/AVG08/Analyse_Simple_Confidence/High_confidence__Low_confidence_vs_HSF_gabor__LSF_gabor The log file is attached. I don't find error in the text. Where am I wrong? Is there any mri_glmfit-sess like script somewhere? It's going to be pretty tough to find each parameter to feed to mri_glmfit... Thanks, Max ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] isxconcat-sess error
Hi, I've been running into a problem when trying to run a group analysis. When I go to run isxconcat-sess, I use this command: isxconcat-sess -sf hc.txt -df sesspar -analysis Ext -c CS+lvsCS-l - percent -o ./HC-Ext-083109 -hemis -trgsubject fsaverage It runs through the whole isxconcat without stopping, and there appears to be the normal outputs. However, when I scroll through the text in the terminal window, the following error appears repeatedly (I think once for every subject, possibly for each hemi of each subject): Reading source surface registration /autofs/space/dinah_001/users/balaji/SUBJECTS_DIR/subjects/ ext005_anat/surf/lh.sphere.reg Done loading source registration surface Reading target registration /autofs/space/dinah_001/users/balaji/SUBJECTS_DIR/subjects/ fsaverage/surf/lh.sphere.reg ERROR: could not find volume /autofs/space/dinah_001/users/balaji/ SUBJECTS_DIR/subjects/fsaverage/surf/../mri/orig. Does it exist? Done loading target registration surface Mapping Surfaces (ext005_anat - fsaverage) When I go to fsaverage's folder, the orig.mgz file does exist, but for some reason, it looks like it's trying to direct it into the surf folder and then back out and into the mri folder and having trouble for some reason. When I try to type in the cd command as it appears (with the /../), it does take me to the mri folder where orig.mgz is stored, so I'm not sure why I get the error. I run into trouble after I run mri_glmfit, when I go to run surf- sess. I get the error: grep: /autofs/space/ricki_001/users/brittany/ext_fmri/HC-Ext-083109/ session.info: No such file or directory ERROR: cannot find /autofs/space/ricki_001/users/brittany/ext_fmri/HC- Ext-083109/ext/register.dat and then it exits. So for some reason, it looks like, even though isxconcat and mri_glmfit run and give outputs, they aren't registering to fsaverage somewhere along the way and are therefore not giving all of the outputs I need. Any idea of what I need to do? Thanks! Garth ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] isxconcat-sess question
Hi Doug, I just tried to type in the command you sent me in the dev environment and got this error: ERROR: Flag -talxfm unrecognized. -a MR-sm6-stc -m mask -o MR-group-allsubjects-sm6-stc/MR-sm6-stc/tal.masks.mgz -interp nearest -fsd bold -talres 2 -talxfm fsl-ta1.xfm -sf sessid_noproblem_all_subjects even though I see this when I type isxconcat-sess -help Volume-based options: -talres res : 1 or 2 mm (def is 2) -talxfm xfmfile : use xfmfile instead of talairach.xfm Thanks, Bill On Tue, 11 Mar 2008, Doug Greve wrote: I've just added something to do this. Add -talxfm fsl-tal.xfm to the cmd line. Live on next dev update. doug Bill Monaco wrote: Hi, I wanted to know if it's possible to run isxconcat-sess but have it use a different talairach transform when it calls mri_vol2vol. Currently the default is mri/transforms/talairach.xfm, but I want it to use one I had outputted from a previous processing step - mri/transforms/fsl-ta1.xfm Is there an easy way to do this? Thanks, Bill -- Bill Monaco Research Assistant MGH East - CNY 149 149 13th Street - 2271 Charlestown, MA 02129 617-726-9128 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] isxconcat-sess question
Hi, I wanted to know if it's possible to run isxconcat-sess but have it use a different talairach transform when it calls mri_vol2vol. Currently the default is mri/transforms/talairach.xfm, but I want it to use one I had outputted from a previous processing step - mri/transforms/fsl-ta1.xfm Is there an easy way to do this? Thanks, Bill -- Bill Monaco Research Assistant MGH East - CNY 149 149 13th Street - 2271 Charlestown, MA 02129 617-726-9128 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] isxconcat-sess question
I've just added something to do this. Add -talxfm fsl-tal.xfm to the cmd line. Live on next dev update. doug Bill Monaco wrote: Hi, I wanted to know if it's possible to run isxconcat-sess but have it use a different talairach transform when it calls mri_vol2vol. Currently the default is mri/transforms/talairach.xfm, but I want it to use one I had outputted from a previous processing step - mri/transforms/fsl-ta1.xfm Is there an easy way to do this? Thanks, Bill -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
