[HCP-Users] help on Simple higher level FEAT analysis
Hi, I am trying to do a simple higher level FEAT analysis on some task fMRI data. I would like to correlate a variable to the motor responses. From https://wiki.humanconnectome.org/display/PublicData/Advice+for+FEAT+Analysis+of+HCP+task+fMRI+data I tried the following Higher-level Analysis FEAT GUI, choose that "Inputs are lower-level FEAT directories". Under "Select FEAT directories", for each participant in your group analysis, enter the paths to the .feat directories for the specific lower-level cope of interest (e.g., /myDATA/100307/MNINonLinear/Results/tfMRI_MOTOR/tfMRI_MOTOR_hp200_s2_level2.feat/GrayordinatesStats/cope13.feat FSL then tells me it can not find the design.fsl file in the directory But if I chose the above directory as the input (/myDATA/100307/MNINonLinear/Results/tfMRI_MOTOR/tfMRI_MOTOR_hp200_s2_level2.feat) FSL tells me the directory contains no stats/cope image Is there an example on how to do this? Thanks Clas 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. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] PreFreeSurfer and FreeSurfer pipelines questions
I think you need to ask that on the FreeSurfer list as that is not an HCP
Pipeline issue. Please tell them what version of FreeSurfer you are using.
Matt.
From: Shachar Gal mailto:gal.shac...@gmail.com>>
Date: Monday, August 20, 2018 at 10:53 AM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: Niv Tik mailto:niv...@gmail.com>>
Subject: Re: [HCP-Users] PreFreeSurfer and FreeSurfer pipelines questions
thanks for the (very) quick response,
added to this mail is the log file
but actually I think now that the reason it carried out until the end is
because I changed the 'set -e' to 'set -x' for debugging.
so, here is the error that arises when we just run it with 'set -e':
dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
Expected in: /usr/lib/libSystem.B.dylib
dyld: Symbol not found: ___emutls_get_address
Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
Expected in: /usr/lib/libSystem.B.dylib
thanks again
Sahchar
On Mon, 20 Aug 2018 at 18:38, Glasser, Matthew
mailto:glass...@wustl.edu>> wrote:
1. You can get the gradient distortion coefficients from your scanner. NONE
can be set and for some scanners it does not make much difference (e.g. Trio).
2. recon_all_seed is a random number seed. Presumably this is an optional
argument, but you could set 12345.
3. Need to look at the recon-all log to see what failed.
4. Give T1w and T2w from the ${StudyFolder}/${Subject}/T1w folder with
acpc_dc_restore.
Matt.
From:
mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of Shachar Gal mailto:gal.shac...@gmail.com>>
Date: Monday, August 20, 2018 at 10:34 AM
To: "hcp-users@humanconnectome.org"
mailto:hcp-users@humanconnectome.org>>
Cc: Niv Tik mailto:niv...@gmail.com>>
Subject: [HCP-Users] PreFreeSurfer and FreeSurfer pipelines questions
Hello dear experts
As I mentioned in an earlier message, we are trying to implement the HCP
pipelines to our data, and we have a few questions.
After some struggling, we successfully ran the PreSurfer Pipeline we tried
running the FreeSurfer Pipeline. we ran in with 'gdcoeffs' set to 'NONE',
because we don't have any file with the gradient distortion coefficients. is
that a problem?
After running the PreFreeSurfer, we tried to run the FreeSurfer pipeline, but
didn't really know what to put as the 'recon_all_seed', so we tried to run the
script without giving it any input.
The script somehow completed running "successfully", but without producing
anything really - the 'surf' folder in the subject's dir is completely empty...
Which brings us to our question - what is the necessary input for
'recon_all_seed'?
And another question just to make sure - the t1 and t2 images we should give
the FreeSurfer pipeline are the acc_dc_restore ones, right?
Hope to hear from you
Shachar Gal, Tel Aviv University
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
The materials in this message are private and may contain Protected Healthcare
Information or other information of a sensitive nature. If you are not the
intended recipient, be advised that any unauthorized use, disclosure, copying
or the taking of any action in reliance on the contents of this information is
strictly prohibited. If you have received this email in error, please
immediately notify the sender via telephone or return mail.
The materials in this message are private and may contain Protected Healthcare
Information or other information of a sensitive nature. If you are not the
intended recipient, be advised that any unauthorized use, disclosure, copying
or the taking of any action in reliance on the contents of this information is
strictly prohibited. If you have received this email in error, please
immediately notify the sender via telephone or return mail.
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] PreFreeSurfer and FreeSurfer pipelines questions
1. You can get the gradient distortion coefficients from your scanner. NONE
can be set and for some scanners it does not make much difference (e.g. Trio).
2. recon_all_seed is a random number seed. Presumably this is an optional
argument, but you could set 12345.
3. Need to look at the recon-all log to see what failed.
4. Give T1w and T2w from the ${StudyFolder}/${Subject}/T1w folder with
acpc_dc_restore.
Matt.
From:
mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of Shachar Gal mailto:gal.shac...@gmail.com>>
Date: Monday, August 20, 2018 at 10:34 AM
To: "hcp-users@humanconnectome.org"
mailto:hcp-users@humanconnectome.org>>
Cc: Niv Tik mailto:niv...@gmail.com>>
Subject: [HCP-Users] PreFreeSurfer and FreeSurfer pipelines questions
Hello dear experts
As I mentioned in an earlier message, we are trying to implement the HCP
pipelines to our data, and we have a few questions.
After some struggling, we successfully ran the PreSurfer Pipeline we tried
running the FreeSurfer Pipeline. we ran in with 'gdcoeffs' set to 'NONE',
because we don't have any file with the gradient distortion coefficients. is
that a problem?
After running the PreFreeSurfer, we tried to run the FreeSurfer pipeline, but
didn't really know what to put as the 'recon_all_seed', so we tried to run the
script without giving it any input.
The script somehow completed running "successfully", but without producing
anything really - the 'surf' folder in the subject's dir is completely empty...
Which brings us to our question - what is the necessary input for
'recon_all_seed'?
And another question just to make sure - the t1 and t2 images we should give
the FreeSurfer pipeline are the acc_dc_restore ones, right?
Hope to hear from you
Shachar Gal, Tel Aviv University
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
The materials in this message are private and may contain Protected Healthcare
Information or other information of a sensitive nature. If you are not the
intended recipient, be advised that any unauthorized use, disclosure, copying
or the taking of any action in reliance on the contents of this information is
strictly prohibited. If you have received this email in error, please
immediately notify the sender via telephone or return mail.
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] help on Simple higher level FEAT analysis
Hi, FSL/FEAT are not currently equipped to handle grayordinate data. We have examples of a “third-level” (across subject) analyses as part of the Practicals in the HCP Course. The content for the 2018 course (in June) will hopefully become available online in the near future. Until then, the material from the 2017 course is available, which covered the same basic content in this regard: https://store.humanconnectome.org/courses/2017/exploring-the-human-connectome.php (see the “tfMRI and PALM” tutorial). Cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: on behalf of "Linnman, Clas,Ph.D." Date: Monday, August 20, 2018 at 11:00 AM To: "hcp-users@humanconnectome.org" Subject: [HCP-Users] help on Simple higher level FEAT analysis Hi, I am trying to do a simple higher level FEAT analysis on some task fMRI data. I would like to correlate a variable to the motor responses. From https://wiki.humanconnectome.org/display/PublicData/Advice+for+FEAT+Analysis+of+HCP+task+fMRI+data I tried the following Higher-level Analysis FEAT GUI, choose that "Inputs are lower-level FEAT directories". Under "Select FEAT directories", for each participant in your group analysis, enter the paths to the .feat directories for the specific lower-level cope of interest (e.g., /myDATA/100307/MNINonLinear/Results/tfMRI_MOTOR/tfMRI_MOTOR_hp200_s2_level2.feat/GrayordinatesStats/cope13.feat FSL then tells me it can not find the design.fsl file in the directory But if I chose the above directory as the input (/myDATA/100307/MNINonLinear/Results/tfMRI_MOTOR/tfMRI_MOTOR_hp200_s2_level2.feat) FSL tells me the directory contains no stats/cope image Is there an example on how to do this? Thanks Clas 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. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
