Re: [Freesurfer] GLM_Fit Question
not sure what you're talking about On 5/16/17 2:55 PM, Mikael Novén wrote: Dear Freesurfer experts, I also have this problem and can’t seem to find the script. Would it be possible to get access to it? Thank you in advance, Mikael Novén ___ 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] GLM_Fit Question
Dear Freesurfer experts, I also have this problem and can't seem to find the script. Would it be possible to get access to it? Thank you in advance, Mikael Novén ___ 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] GLM_Fit Question
try now On 6/16/16 11:50 PM, Arkadiy Maksimovskiy wrote: Hi Freesurfers, I am having a similar problem with the FSGD file as the user indicated at this thread: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40599.html I am trying to access the script that Doug wrote in order to fix it, however, the link to download the script does not seem to be working. I was wondering if someone might be able to upload it again. Thank you in advance for your help, Arkadiy ___ 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] GLM_Fit Question
Hi Freesurfers, I am having a similar problem with the FSGD file as the user indicated at this thread: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40599.html I am trying to access the script that Doug wrote in order to fix it, however, the link to download the script does not seem to be working. I was wondering if someone might be able to upload it again. Thank you in advance for your help, Arkadiy ___ 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] GLM_Fit Question
Thanks so much! That did the trick. Taylor Elrod ___ 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] GLM_Fit Question
I've created a new script to remove the carriage returns in your file. You can get it from here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/rmcr copy it into $FREESURFER_HOME/bin (or anywhere in your path), rehash, then run rmcr ABIDE_10K_2.fsgd > new.ABIDE_10K_2.fsgd On 03/24/2015 05:31 PM, Elrod, Christian - SJHMC wrote: > Yes. I attached the original and the newly created one to this email. > > Thanks, > Taylor Elrod > Research Assistant > Human Brain Imaging Lab > Barrow Neurological Institute > > Dignity Health > St. Joseph's Hospital and Medical Center > 222 West Thomas Rd > Phoenix, AZ 85013 > > (O) 602-746-4494 > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Tuesday, March 24, 2015 2:25 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] GLM_Fit Question > > The error is in the fsgd file. Can you send it to me? > > On 03/24/2015 05:16 PM, Elrod, Christian - SJHMC wrote: >> Dr. Greve, >> >> Thank you for your response. I am not using a windows machine for freesurfer >> but a Mac with OS 10.8.5 running Freesurfer V 5.3.0. I created a new .fsgd >> as outlined in your previous response and am still receiving an identical >> error message. Is it possible that there is an error with my contrast file? >> >> ABIDE_10k_2.mtx >> >> -1 1 1 -1 0 0 0 0 >> >> >> Taylor Elrod >> Research Assistant >> Human Brain Imaging Lab >> Barrow Neurological Institute >> >> Dignity Health >> St. Joseph's Hospital and Medical Center >> 222 West Thomas Rd >> Phoenix, AZ 85013 >> >> (O) 602-746-4494 >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve >> [gr...@nmr.mgh.harvard.edu] >> Sent: Monday, March 23, 2015 9:32 AM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] GLM_Fit Question >> >> The format of the fsgd file looks ok, but I suspect that there is a >> platform issue. How did you create it? Under windows? You can try >> something like >> >> cat your.fsgd | sed 's/\\r/\\n/g' > new.your.fsgd >> >> use new.your.fsgd and see if this fixes the problem. >> >> On 03/20/2015 02:48 PM, Elrod, Christian - SJHMC wrote: >>> Hello Freesurfer Group, >>> >>> I have a question regarding an error that I have been receiving when >>> attempting to set up an analysis involving 4 groups of subjects with data >>> coming from 2 separate scanning sites. The error is "ERROR: gdfReadV1: >>> Found 7 variables, expected 1". This is how it appears in terminal when >>> coding for GLM_fit: >>> >>> drs-mac-pro:ABIDE_10K_2 FMRI$ mri_glmfit --y lh.ABIDE_10K_2.00.mgh >>> --fsgd ABIDE_10K_2.fsgd dods --C ABIDE_10k_2.mtx --surf fsaverage lh >>> --cortex >>> gdfReadHeader: reading ABIDE_10K_2.fsgd >>> ERROR: gdfReadV1: Input line 1, subjid = 51480_out >>> Found 7 variables, expected. 1 >>> FSGDF Format Error: file = ABIDE_10K_2.fsgd, tag=Input >>> >>> >>> However, in the fsgd file, modeled after the example shown here ( >>> https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V ) for 4 groups with one >>> co-variate, I have only established one variable (to my knowledge) and >>> cannot seem to figure out why I keep receiving this error. Here is a copy >>> of the beginning of the fsgd file that is being utilized for the mri_glmfit >>> command: >>> >>> GroupDescriptorFile 1 >>> Title ABIDE_ASD_X_Age >>> Class ControlYoung >>> Class ControlOld >>> Class ASDYoung >>> Class ASDOld >>> Variables Site >>> Input 51480_out ControlYoung 1 >>> Input 51484_out ControlYoung 1 >>> Input 51485_out ControlYoung 1 >>> Input 50657_out ControlYoung 1 >>> Input 50688_out ControlYoung 1 >>> Input 50699_out ControlYoung 1 >>> Input 51333_out ControlYoung 1 >>> Input 10006_FSoutput ControlOld 2 >>> Input 10009_FSoutput ControlOld 2 >>> Input 10011_FSoutput ControlOld 2 >>> Input 10013_FSoutput ControlOld 2 >>> Input 10014_FSoutput ControlOld 2 >>> . >>> >>> Any help or suggestions would be greatly appreciated. >>> >>> Thanks, >>> Taylo
Re: [Freesurfer] GLM_Fit Question
Yes. I attached the original and the newly created one to this email. Thanks, Taylor Elrod Research Assistant Human Brain Imaging Lab Barrow Neurological Institute Dignity Health St. Joseph's Hospital and Medical Center 222 West Thomas Rd Phoenix, AZ 85013 (O) 602-746-4494 From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Tuesday, March 24, 2015 2:25 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] GLM_Fit Question The error is in the fsgd file. Can you send it to me? On 03/24/2015 05:16 PM, Elrod, Christian - SJHMC wrote: > Dr. Greve, > > Thank you for your response. I am not using a windows machine for freesurfer > but a Mac with OS 10.8.5 running Freesurfer V 5.3.0. I created a new .fsgd as > outlined in your previous response and am still receiving an identical error > message. Is it possible that there is an error with my contrast file? > > ABIDE_10k_2.mtx > > -1 1 1 -1 0 0 0 0 > > > Taylor Elrod > Research Assistant > Human Brain Imaging Lab > Barrow Neurological Institute > > Dignity Health > St. Joseph's Hospital and Medical Center > 222 West Thomas Rd > Phoenix, AZ 85013 > > (O) 602-746-4494 > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Monday, March 23, 2015 9:32 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] GLM_Fit Question > > The format of the fsgd file looks ok, but I suspect that there is a > platform issue. How did you create it? Under windows? You can try > something like > > cat your.fsgd | sed 's/\\r/\\n/g' > new.your.fsgd > > use new.your.fsgd and see if this fixes the problem. > > On 03/20/2015 02:48 PM, Elrod, Christian - SJHMC wrote: >> Hello Freesurfer Group, >> >> I have a question regarding an error that I have been receiving when >> attempting to set up an analysis involving 4 groups of subjects with data >> coming from 2 separate scanning sites. The error is "ERROR: gdfReadV1: >> Found 7 variables, expected 1". This is how it appears in terminal when >> coding for GLM_fit: >> >> drs-mac-pro:ABIDE_10K_2 FMRI$ mri_glmfit --y lh.ABIDE_10K_2.00.mgh >> --fsgd ABIDE_10K_2.fsgd dods --C ABIDE_10k_2.mtx --surf fsaverage lh >> --cortex >> gdfReadHeader: reading ABIDE_10K_2.fsgd >> ERROR: gdfReadV1: Input line 1, subjid = 51480_out >> Found 7 variables, expected. 1 >> FSGDF Format Error: file = ABIDE_10K_2.fsgd, tag=Input >> >> >> However, in the fsgd file, modeled after the example shown here ( >> https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V ) for 4 groups with one >> co-variate, I have only established one variable (to my knowledge) and >> cannot seem to figure out why I keep receiving this error. Here is a copy of >> the beginning of the fsgd file that is being utilized for the mri_glmfit >> command: >> >> GroupDescriptorFile 1 >> Title ABIDE_ASD_X_Age >> Class ControlYoung >> Class ControlOld >> Class ASDYoung >> Class ASDOld >> Variables Site >> Input 51480_out ControlYoung 1 >> Input 51484_out ControlYoung 1 >> Input 51485_out ControlYoung 1 >> Input 50657_out ControlYoung 1 >> Input 50688_out ControlYoung 1 >> Input 50699_out ControlYoung 1 >> Input 51333_out ControlYoung 1 >> Input 10006_FSoutput ControlOld 2 >> Input 10009_FSoutput ControlOld 2 >> Input 10011_FSoutput ControlOld 2 >> Input 10013_FSoutput ControlOld 2 >> Input 10014_FSoutput ControlOld 2 >> . >> >> Any help or suggestions would be greatly appreciated. >> >> Thanks, >> Taylor Elrod >> >> >> ___ >> 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/frees
Re: [Freesurfer] GLM_Fit Question
The error is in the fsgd file. Can you send it to me? On 03/24/2015 05:16 PM, Elrod, Christian - SJHMC wrote: > Dr. Greve, > > Thank you for your response. I am not using a windows machine for freesurfer > but a Mac with OS 10.8.5 running Freesurfer V 5.3.0. I created a new .fsgd as > outlined in your previous response and am still receiving an identical error > message. Is it possible that there is an error with my contrast file? > > ABIDE_10k_2.mtx > > -1 1 1 -1 0 0 0 0 > > > Taylor Elrod > Research Assistant > Human Brain Imaging Lab > Barrow Neurological Institute > > Dignity Health > St. Joseph's Hospital and Medical Center > 222 West Thomas Rd > Phoenix, AZ 85013 > > (O) 602-746-4494 > (C) 804-399-8674 > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Monday, March 23, 2015 9:32 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] GLM_Fit Question > > The format of the fsgd file looks ok, but I suspect that there is a > platform issue. How did you create it? Under windows? You can try > something like > > cat your.fsgd | sed 's/\\r/\\n/g' > new.your.fsgd > > use new.your.fsgd and see if this fixes the problem. > > On 03/20/2015 02:48 PM, Elrod, Christian - SJHMC wrote: >> Hello Freesurfer Group, >> >> I have a question regarding an error that I have been receiving when >> attempting to set up an analysis involving 4 groups of subjects with data >> coming from 2 separate scanning sites. The error is "ERROR: gdfReadV1: >> Found 7 variables, expected 1". This is how it appears in terminal when >> coding for GLM_fit: >> >> drs-mac-pro:ABIDE_10K_2 FMRI$ mri_glmfit --y lh.ABIDE_10K_2.00.mgh >> --fsgd ABIDE_10K_2.fsgd dods --C ABIDE_10k_2.mtx --surf fsaverage lh >> --cortex >> gdfReadHeader: reading ABIDE_10K_2.fsgd >> ERROR: gdfReadV1: Input line 1, subjid = 51480_out >> Found 7 variables, expected. 1 >> FSGDF Format Error: file = ABIDE_10K_2.fsgd, tag=Input >> >> >> However, in the fsgd file, modeled after the example shown here ( >> https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V ) for 4 groups with one >> co-variate, I have only established one variable (to my knowledge) and >> cannot seem to figure out why I keep receiving this error. Here is a copy of >> the beginning of the fsgd file that is being utilized for the mri_glmfit >> command: >> >> GroupDescriptorFile 1 >> Title ABIDE_ASD_X_Age >> Class ControlYoung >> Class ControlOld >> Class ASDYoung >> Class ASDOld >> Variables Site >> Input 51480_out ControlYoung 1 >> Input 51484_out ControlYoung 1 >> Input 51485_out ControlYoung 1 >> Input 50657_out ControlYoung 1 >> Input 50688_out ControlYoung 1 >> Input 50699_out ControlYoung 1 >> Input 51333_out ControlYoung 1 >> Input 10006_FSoutput ControlOld 2 >> Input 10009_FSoutput ControlOld 2 >> Input 10011_FSoutput ControlOld 2 >> Input 10013_FSoutput ControlOld 2 >> Input 10014_FSoutput ControlOld 2 >> . >> >> Any help or suggestions would be greatly appreciated. >> >> Thanks, >> Taylor Elrod >> >> >> ___ >> 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. > > > ___ > Freesurfer mailing lis
Re: [Freesurfer] GLM_Fit Question
Dr. Greve, Thank you for your response. I am not using a windows machine for freesurfer but a Mac with OS 10.8.5 running Freesurfer V 5.3.0. I created a new .fsgd as outlined in your previous response and am still receiving an identical error message. Is it possible that there is an error with my contrast file? ABIDE_10k_2.mtx -1 1 1 -1 0 0 0 0 Taylor Elrod Research Assistant Human Brain Imaging Lab Barrow Neurological Institute Dignity Health St. Joseph's Hospital and Medical Center 222 West Thomas Rd Phoenix, AZ 85013 (O) 602-746-4494 (C) 804-399-8674 From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, March 23, 2015 9:32 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] GLM_Fit Question The format of the fsgd file looks ok, but I suspect that there is a platform issue. How did you create it? Under windows? You can try something like cat your.fsgd | sed 's/\\r/\\n/g' > new.your.fsgd use new.your.fsgd and see if this fixes the problem. On 03/20/2015 02:48 PM, Elrod, Christian - SJHMC wrote: > Hello Freesurfer Group, > > I have a question regarding an error that I have been receiving when > attempting to set up an analysis involving 4 groups of subjects with data > coming from 2 separate scanning sites. The error is "ERROR: gdfReadV1: Found > 7 variables, expected 1". This is how it appears in terminal when coding for > GLM_fit: > > drs-mac-pro:ABIDE_10K_2 FMRI$ mri_glmfit --y lh.ABIDE_10K_2.00.mgh --fsgd > ABIDE_10K_2.fsgd dods --C ABIDE_10k_2.mtx --surf fsaverage lh --cortex > gdfReadHeader: reading ABIDE_10K_2.fsgd > ERROR: gdfReadV1: Input line 1, subjid = 51480_out > Found 7 variables, expected. 1 > FSGDF Format Error: file = ABIDE_10K_2.fsgd, tag=Input > > > However, in the fsgd file, modeled after the example shown here ( > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V ) for 4 groups with one > co-variate, I have only established one variable (to my knowledge) and cannot > seem to figure out why I keep receiving this error. Here is a copy of the > beginning of the fsgd file that is being utilized for the mri_glmfit command: > > GroupDescriptorFile 1 > Title ABIDE_ASD_X_Age > Class ControlYoung > Class ControlOld > Class ASDYoung > Class ASDOld > Variables Site > Input 51480_out ControlYoung 1 > Input 51484_out ControlYoung 1 > Input 51485_out ControlYoung 1 > Input 50657_out ControlYoung 1 > Input 50688_out ControlYoung 1 > Input 50699_out ControlYoung 1 > Input 51333_out ControlYoung 1 > Input 10006_FSoutput ControlOld 2 > Input 10009_FSoutput ControlOld 2 > Input 10011_FSoutput ControlOld 2 > Input 10013_FSoutput ControlOld 2 > Input 10014_FSoutput ControlOld 2 > . > > Any help or suggestions would be greatly appreciated. > > Thanks, > Taylor Elrod > > > ___ > 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] GLM_Fit Question
The format of the fsgd file looks ok, but I suspect that there is a platform issue. How did you create it? Under windows? You can try something like cat your.fsgd | sed 's/\\r/\\n/g' > new.your.fsgd use new.your.fsgd and see if this fixes the problem. On 03/20/2015 02:48 PM, Elrod, Christian - SJHMC wrote: > Hello Freesurfer Group, > > I have a question regarding an error that I have been receiving when > attempting to set up an analysis involving 4 groups of subjects with data > coming from 2 separate scanning sites. The error is "ERROR: gdfReadV1: Found > 7 variables, expected 1". This is how it appears in terminal when coding for > GLM_fit: > > drs-mac-pro:ABIDE_10K_2 FMRI$ mri_glmfit --y lh.ABIDE_10K_2.00.mgh --fsgd > ABIDE_10K_2.fsgd dods --C ABIDE_10k_2.mtx --surf fsaverage lh --cortex > gdfReadHeader: reading ABIDE_10K_2.fsgd > ERROR: gdfReadV1: Input line 1, subjid = 51480_out > Found 7 variables, expected. 1 > FSGDF Format Error: file = ABIDE_10K_2.fsgd, tag=Input > > > However, in the fsgd file, modeled after the example shown here ( > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V ) for 4 groups with one > co-variate, I have only established one variable (to my knowledge) and cannot > seem to figure out why I keep receiving this error. Here is a copy of the > beginning of the fsgd file that is being utilized for the mri_glmfit command: > > GroupDescriptorFile 1 > Title ABIDE_ASD_X_Age > Class ControlYoung > Class ControlOld > Class ASDYoung > Class ASDOld > Variables Site > Input 51480_out ControlYoung 1 > Input 51484_out ControlYoung 1 > Input 51485_out ControlYoung 1 > Input 50657_out ControlYoung 1 > Input 50688_out ControlYoung 1 > Input 50699_out ControlYoung 1 > Input 51333_out ControlYoung 1 > Input 10006_FSoutput ControlOld 2 > Input 10009_FSoutput ControlOld 2 > Input 10011_FSoutput ControlOld 2 > Input 10013_FSoutput ControlOld 2 > Input 10014_FSoutput ControlOld 2 > . > > Any help or suggestions would be greatly appreciated. > > Thanks, > Taylor Elrod > > > ___ > 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.
[Freesurfer] GLM_Fit Question
Hello Freesurfer Group, I have a question regarding an error that I have been receiving when attempting to set up an analysis involving 4 groups of subjects with data coming from 2 separate scanning sites. The error is "ERROR: gdfReadV1: Found 7 variables, expected 1". This is how it appears in terminal when coding for GLM_fit: drs-mac-pro:ABIDE_10K_2 FMRI$ mri_glmfit --y lh.ABIDE_10K_2.00.mgh --fsgd ABIDE_10K_2.fsgd dods --C ABIDE_10k_2.mtx --surf fsaverage lh --cortex gdfReadHeader: reading ABIDE_10K_2.fsgd ERROR: gdfReadV1: Input line 1, subjid = 51480_out Found 7 variables, expected. 1 FSGDF Format Error: file = ABIDE_10K_2.fsgd, tag=Input However, in the fsgd file, modeled after the example shown here ( https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V ) for 4 groups with one co-variate, I have only established one variable (to my knowledge) and cannot seem to figure out why I keep receiving this error. Here is a copy of the beginning of the fsgd file that is being utilized for the mri_glmfit command: GroupDescriptorFile 1 Title ABIDE_ASD_X_Age Class ControlYoung Class ControlOld Class ASDYoung Class ASDOld Variables Site Input 51480_out ControlYoung 1 Input 51484_out ControlYoung 1 Input 51485_out ControlYoung 1 Input 50657_out ControlYoung 1 Input 50688_out ControlYoung 1 Input 50699_out ControlYoung 1 Input 51333_out ControlYoung 1 Input 10006_FSoutput ControlOld 2 Input 10009_FSoutput ControlOld 2 Input 10011_FSoutput ControlOld 2 Input 10013_FSoutput ControlOld 2 Input 10014_FSoutput ControlOld 2 . Any help or suggestions would be greatly appreciated. Thanks, Taylor Elrod ___ 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] glm_fit question...
Cameron Ellis wrote: Hi all, Is it necessary to include a value in your contrast matrix for every class and variable in your fsgd file? Yes, you have to have a value in the contrast matrix for each regressor in the design matrix. It seems that this is the case. My understanding is that if you weight a variable 0 then it is automatically controlled for. So if am required to weight a variabe in the contrast matrix that do not want to control for, then to not control for it I have to make a different fsgd file without that variable? Yes, if you do not want to control for a variable then leave it out of the analysis entirely. doug Thanks, Cameron ___ 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 [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
[Freesurfer] glm_fit question...
Hi all, Is it necessary to include a value in your contrast matrix for every class and variable in your fsgd file? It seems that this is the case. My understanding is that if you weight a variable 0 then it is automatically controlled for. So if am required to weight a variabe in the contrast matrix that do not want to control for, then to not control for it I have to make a different fsgd file without that variable? Thanks, Cameron ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
