Hi Freesurfer users.
I am currently performing the steps of Functional Connectivity Walkthrough. And after resolving the problems in the first steps, specially in the preprocessing command (missing AFNI files), I'm now stuck in the 5th step: Creating the FC seeds for each subject.
In the 4th step I've created the parameters for a region of interest. In this case, cheking the FreeSurferColorLUT.txt, I run this command to create the parameters for Left CA1 of Hippocampus (after the reconstruction, I performed the hippocampal subfields):
fcseed-config -segid 552 -fcname L_CA1.dat -fsd rest -mean -cfg
mean.L_CA1.config
In the 5th step, when I run the fcseed-sess command, I obtain this error and I'm unable to figure out why:
fcseed-sess -s con_algon -cfg L_CA1.config
ERROR: could not determine file for
/Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/fmcpr stem2fname /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/fmcpr
I've checked the "009" folder and there isn't any file with the name "fmcpr".
Does someone have any idea how could I resolve this?
Thanks!
Hi Julio, In the past I received this error because the subject was not preprocessed correctly. Make sure you have a link to the subject's structural recon folder in the resting state folder. In order to do this, you have to create a txt file(in this case it would 02_resting/subjectname) and within that txt file you put the name of the recon directory. After doing this, make sure that the $SUBJECTS_DIR is where the subject's recon folder is or else it won't fully run preprocessing. Hope this helps! Best, Talia ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Julio Alberto González Torre [al099821@uji.es] Sent: Thursday, April 14, 2016 6:42 PM To: Freesurfer support list Subject: [Freesurfer] fcseed-sess ERROR: could not determine file for .../fmcpr
Hi Freesurfer users.
I am currently performing the steps of Functional Connectivity Walkthrough. And after resolving the problems in the first steps, specially in the preprocessing command (missing AFNI files), I'm now stuck in the 5th step: Creating the FC seeds for each subject.
In the 4th step I've created the parameters for a region of interest. In this case, cheking the FreeSurferColorLUT.txt, I run this command to create the parameters for Left CA1 of Hippocampus (after the reconstruction, I performed the hippocampal subfields):
fcseed-config -segid 552 -fcname L_CA1.dat -fsd rest -mean -cfg mean.L_CA1.config
In the 5th step, when I run the fcseed-sess command, I obtain this error and I'm unable to figure out why:
fcseed-sess -s con_algon -cfg L_CA1.config
ERROR: could not determine file for /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/fmcpr stem2fname /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/fmcpr
I've checked the "009" folder and there isn't any file with the name "fmcpr".
Does someone have any idea how could I resolve this?
Thanks!
Hi Talia. Thanks for the quick answer.
But the preprocessing finished correctly without errors as I can check on all the log files generated in the same project folder. "subjectname" and $SUBJECTS_DIR are correctly placed.
The problem is a later step (STEP 5, http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthr...), when I try to create FC seeds for an individual.
As long as I can read in previously threads, the problem may be the parameter "-per-session", so now I'm trying to do it with "-per-run" parameter to check if the error remains. But I was unable to find a definitive fix for this error.
2016-04-15 14:09 GMT+02:00 Raney, Talia L. TRANEY@partners.org:
Hi Julio, In the past I received this error because the subject was not preprocessed correctly. Make sure you have a link to the subject's structural recon folder in the resting state folder. In order to do this, you have to create a txt file(in this case it would 02_resting/subjectname) and within that txt file you put the name of the recon directory. After doing this, make sure that the $SUBJECTS_DIR is where the subject's recon folder is or else it won't fully run preprocessing. Hope this helps! Best, Talia ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Julio Alberto González Torre [al099821@uji.es] Sent: Thursday, April 14, 2016 6:42 PM To: Freesurfer support list Subject: [Freesurfer] fcseed-sess ERROR: could not determine file for .../fmcpr
Hi Freesurfer users.
I am currently performing the steps of Functional Connectivity Walkthrough. And after resolving the problems in the first steps, specially in the preprocessing command (missing AFNI files), I'm now stuck in the 5th step: Creating the FC seeds for each subject.
In the 4th step I've created the parameters for a region of interest. In this case, cheking the FreeSurferColorLUT.txt, I run this command to create the parameters for Left CA1 of Hippocampus (after the reconstruction, I performed the hippocampal subfields):
fcseed-config -segid 552 -fcname L_CA1.dat -fsd rest -mean -cfg mean.L_CA1.config
In the 5th step, when I run the fcseed-sess command, I obtain this error and I'm unable to figure out why:
fcseed-sess -s con_algon -cfg L_CA1.config
ERROR: could not determine file for /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/fmcpr stem2fname /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/fmcpr
I've checked the "009" folder and there isn't any file with the name "fmcpr".
Does someone have any idea how could I resolve this?
Thanks!
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.
Hi Julio, You're right in that the problem is occurring in a later step. However, the fmcpr file is created during preprocessing. When you do the preprocessing step, it doesn't show an error occurring in the logs(this happened to me too because it said that preproc-sess was completed but fcseed-sess gave me this error that it could not determine the fmcpr file). You're right that you have to use the per-run parameter during preproc-sess. I think this will fix the problem if everything else is set up correctly. Best, Talia ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Julio Alberto González Torre [al099821@uji.es] Sent: Friday, April 15, 2016 11:42 AM To: Freesurfer support list Subject: Re: [Freesurfer] fcseed-sess ERROR: could not determine file for .../fmcpr
Hi Talia. Thanks for the quick answer.
But the preprocessing finished correctly without errors as I can check on all the log files generated in the same project folder. "subjectname" and $SUBJECTS_DIR are correctly placed.
The problem is a later step (STEP 5, http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthr...), when I try to create FC seeds for an individual.
As long as I can read in previously threads, the problem may be the parameter "-per-session", so now I'm trying to do it with "-per-run" parameter to check if the error remains. But I was unable to find a definitive fix for this error.
2016-04-15 14:09 GMT+02:00 Raney, Talia L. <TRANEY@partners.orgmailto:TRANEY@partners.org>: Hi Julio, In the past I received this error because the subject was not preprocessed correctly. Make sure you have a link to the subject's structural recon folder in the resting state folder. In order to do this, you have to create a txt file(in this case it would 02_resting/subjectname) and within that txt file you put the name of the recon directory. After doing this, make sure that the $SUBJECTS_DIR is where the subject's recon folder is or else it won't fully run preprocessing. Hope this helps! Best, Talia ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Julio Alberto González Torre [al099821@uji.esmailto:al099821@uji.es] Sent: Thursday, April 14, 2016 6:42 PM To: Freesurfer support list Subject: [Freesurfer] fcseed-sess ERROR: could not determine file for .../fmcpr
Hi Freesurfer users.
I am currently performing the steps of Functional Connectivity Walkthrough. And after resolving the problems in the first steps, specially in the preprocessing command (missing AFNI files), I'm now stuck in the 5th step: Creating the FC seeds for each subject.
In the 4th step I've created the parameters for a region of interest. In this case, cheking the FreeSurferColorLUT.txt, I run this command to create the parameters for Left CA1 of Hippocampus (after the reconstruction, I performed the hippocampal subfields):
fcseed-config -segid 552 -fcname L_CA1.dat -fsd rest -mean -cfg mean.L_CA1.config
In the 5th step, when I run the fcseed-sess command, I obtain this error and I'm unable to figure out why:
fcseed-sess -s con_algon -cfg L_CA1.config
ERROR: could not determine file for /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/fmcpr stem2fname /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/fmcpr
I've checked the "009" folder and there isn't any file with the name "fmcpr".
Does someone have any idea how could I resolve this?
Thanks!
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.
I performed the preprocessing again with -per-run parameter. Everything ok in that step.
The, when I run the fcseed-sess command, I've got new errors.
Segmentation fault
MRIalloc(0, 1, 1): bad parm
I have attached the log file.
2016-04-15 17:56 GMT+02:00 Raney, Talia L. TRANEY@partners.org:
Hi Julio, You're right in that the problem is occurring in a later step. However, the fmcpr file is created during preprocessing. When you do the preprocessing step, it doesn't show an error occurring in the logs(this happened to me too because it said that preproc-sess was completed but fcseed-sess gave me this error that it could not determine the fmcpr file). You're right that you have to use the per-run parameter during preproc-sess. I think this will fix the problem if everything else is set up correctly. Best, Talia ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Julio Alberto González Torre [al099821@uji.es] Sent: Friday, April 15, 2016 11:42 AM To: Freesurfer support list Subject: Re: [Freesurfer] fcseed-sess ERROR: could not determine file for .../fmcpr
Hi Talia. Thanks for the quick answer.
But the preprocessing finished correctly without errors as I can check on all the log files generated in the same project folder. "subjectname" and $SUBJECTS_DIR are correctly placed.
The problem is a later step (STEP 5, http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthr...), when I try to create FC seeds for an individual.
As long as I can read in previously threads, the problem may be the parameter "-per-session", so now I'm trying to do it with "-per-run" parameter to check if the error remains. But I was unable to find a definitive fix for this error.
2016-04-15 14:09 GMT+02:00 Raney, Talia L. <TRANEY@partners.orgmailto: TRANEY@partners.org>: Hi Julio, In the past I received this error because the subject was not preprocessed correctly. Make sure you have a link to the subject's structural recon folder in the resting state folder. In order to do this, you have to create a txt file(in this case it would 02_resting/subjectname) and within that txt file you put the name of the recon directory. After doing this, make sure that the $SUBJECTS_DIR is where the subject's recon folder is or else it won't fully run preprocessing. Hope this helps! Best, Talia ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto: freesurfer-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edumailto: freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Julio Alberto González Torre [al099821@uji.esmailto:al099821@uji.es] Sent: Thursday, April 14, 2016 6:42 PM To: Freesurfer support list Subject: [Freesurfer] fcseed-sess ERROR: could not determine file for .../fmcpr
Hi Freesurfer users.
I am currently performing the steps of Functional Connectivity Walkthrough. And after resolving the problems in the first steps, specially in the preprocessing command (missing AFNI files), I'm now stuck in the 5th step: Creating the FC seeds for each subject.
In the 4th step I've created the parameters for a region of interest. In this case, cheking the FreeSurferColorLUT.txt, I run this command to create the parameters for Left CA1 of Hippocampus (after the reconstruction, I performed the hippocampal subfields):
fcseed-config -segid 552 -fcname L_CA1.dat -fsd rest -mean -cfg mean.L_CA1.config
In the 5th step, when I run the fcseed-sess command, I obtain this error and I'm unable to figure out why:
fcseed-sess -s con_algon -cfg L_CA1.config
ERROR: could not determine file for /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/fmcpr stem2fname /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/fmcpr
I've checked the "009" folder and there isn't any file with the name "fmcpr".
Does someone have any idea how could I resolve this?
Thanks!
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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
That means that there are no voxels in the final ROI in native functional space. You should check your registration and also see how big your original ROI is.
On 04/15/2016 11:32 PM, Julio Alberto González Torre wrote:
I performed the preprocessing again with -per-run parameter. Everything ok in that step.
The, when I run the fcseed-sess command, I've got new errors.
Segmentation fault
MRIalloc(0, 1, 1): bad parm
I have attached the log file.
2016-04-15 17:56 GMT+02:00 Raney, Talia L. <TRANEY@partners.org mailto:TRANEY@partners.org>:
Hi Julio, You're right in that the problem is occurring in a later step. However, the fmcpr file is created during preprocessing. When you do the preprocessing step, it doesn't show an error occurring in the logs(this happened to me too because it said that preproc-sess was completed but fcseed-sess gave me this error that it could not determine the fmcpr file). You're right that you have to use the per-run parameter during preproc-sess. I think this will fix the problem if everything else is set up correctly. Best, Talia ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Julio Alberto González Torre [al099821@uji.es <mailto:al099821@uji.es>] Sent: Friday, April 15, 2016 11:42 AM To: Freesurfer support list Subject: Re: [Freesurfer] fcseed-sess ERROR: could not determine file for .../fmcpr Hi Talia. Thanks for the quick answer. But the preprocessing finished correctly without errors as I can check on all the log files generated in the same project folder. "subjectname" and $SUBJECTS_DIR are correctly placed. The problem is a later step (STEP 5, http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough), when I try to create FC seeds for an individual. As long as I can read in previously threads, the problem may be the parameter "-per-session", so now I'm trying to do it with "-per-run" parameter to check if the error remains. But I was unable to find a definitive fix for this error. 2016-04-15 14:09 GMT+02:00 Raney, Talia L. <TRANEY@partners.org <mailto:TRANEY@partners.org><mailto:TRANEY@partners.org <mailto:TRANEY@partners.org>>>: Hi Julio, In the past I received this error because the subject was not preprocessed correctly. Make sure you have a link to the subject's structural recon folder in the resting state folder. In order to do this, you have to create a txt file(in this case it would 02_resting/subjectname) and within that txt file you put the name of the recon directory. After doing this, make sure that the $SUBJECTS_DIR is where the subject's recon folder is or else it won't fully run preprocessing. Hope this helps! Best, Talia ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu><mailto:freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu><mailto:freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>] on behalf of Julio Alberto González Torre [al099821@uji.es <mailto:al099821@uji.es><mailto:al099821@uji.es <mailto:al099821@uji.es>>] Sent: Thursday, April 14, 2016 6:42 PM To: Freesurfer support list Subject: [Freesurfer] fcseed-sess ERROR: could not determine file for .../fmcpr Hi Freesurfer users. I am currently performing the steps of Functional Connectivity Walkthrough. And after resolving the problems in the first steps, specially in the preprocessing command (missing AFNI files), I'm now stuck in the 5th step: Creating the FC seeds for each subject. In the 4th step I've created the parameters for a region of interest. In this case, cheking the FreeSurferColorLUT.txt, I run this command to create the parameters for Left CA1 of Hippocampus (after the reconstruction, I performed the hippocampal subfields): fcseed-config -segid 552 -fcname L_CA1.dat -fsd rest -mean -cfg mean.L_CA1.config In the 5th step, when I run the fcseed-sess command, I obtain this error and I'm unable to figure out why: fcseed-sess -s con_algon -cfg L_CA1.config ERROR: could not determine file for /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/fmcpr stem2fname /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/fmcpr I've checked the "009" folder and there isn't any file with the name "fmcpr". Does someone have any idea how could I resolve this? Thanks! _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Julio Alberto González Torre -
Raney, Talia L.