[Freesurfer] recon_checker error
Opensuse 11.4 : Freesurfer 5.3 :QAtools_v1.1 I am trying to generate QC data from data generated using Freesurfer ver 5.3 and I'm getting the following error " Checking if all files exist...PASSED Checking actual file order...FAILED (read ../1006454_20216_2_0/scripts/recon_checker.log) ERROR: Actual file order disagrees with common file order for subject 1006454_20216_2_0" On checking the recon_checker.log it states This subject may have been processed with a different version of FreeSurfer other than the version used to create the common file order file (based on v5.1 by default if not specified by the user). Consider generating an output file order file for your specific dataset using the 'genoutputorderfile' flag. See the '-help' flag for details. I cannot find any details of this flag in any help file or any online help as to how to correct his problem Dave Liewald The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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] Longitudinal analysis--mass univariate {Disarmed}
Dear Dr Martin ,
Thanks a lot for your kindness and your great answers!!
Please I have one more question regarding the design matrix:
If I use my design matrix for LME depending on the exampels mentioned in FS wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
Is this correct?
Bests,
John
Sent: Saturday, January 30, 2016 at 5:51 AM
From: "Martin Reuter"
To: "Freesurfer support list"
Subject: Re: [Freesurfer] Longitudinal analysis--mass univariate {Disarmed}
Hi John,
What I mean is there could be a bias in your study design if 99% of group 1 have three or more time points and 99% of group 2 have only two time points. This is something you should check. If distributions are approximately similar, you’d be fine. LME can be used in either case. If there is any biases (also age, gender etc) you’d probably want to control for it via additional co-variates in your LME model.
Best, Martin
On Jan 28, 2016, at 1:12 PM, John Anderson wrote:
Thanks a lot D martin for your quick answer.
Regarding my patients I have two groups but the subject in every group have differnt time points. i.e Group-patients 1: I have 100 patients some scanned three times and some four times the rest at least two times.
Group-Patients 2: is consisted of 75 patients some also some scanned three times and some four times the rest at least two times.
Is LME -- mas usnivariate still workable with out a bias ?
Bests,
John
Sent: Thursday, January 28, 2016 at 6:51 AM
From: "Martin Reuter"
To: "Freesurfer support list"
Subject: Re: [Freesurfer] Longitudinal analysis--mass univariate
Hi John,
you should check if the number of time points per subject is relatively random across your two patient groups. You don’t want a bias, let’s say one patient group with 2 tp and the other with 3.
You can compare the atrophy across these two groups easily with LME. Or you can also test if the rate is different from zero in each individual group.
You will never be able to compute atrophy rates for your control group (as you only have a single time point for them) so you cannot compare with them either.
Best, Martin
On Jan 28, 2016, at 12:23 PM, John Anderson wrote:
Hi Dr Martin,
I have two groups of patients and one group of controls.
The patients scanned multiple times but the number of time points is different between the subjects.
The controls have only one time point.
I aim to :
1. I wanted to study the changes in cortical thickness over time in each group of patients.
2. I wanted to compare the change in cortical thickness between patients and controls over time.
I followed wiki and I choose LME to run the analysis.
My questions are:
1. Can I use mass univariate analysis to check the changes in cortical thickness over time in only one group of patients. The example In wiki was for four groups.
2. Can I do a comparison in cortical thickness over time between controls ( who have only one time point ) and patients using mass univariate approach.
Bests,
John
___
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 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 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
[Freesurfer] mri_vol2surf Averaging with exclusion of specific values
Dear FreeSurfer expert, I would like to project my maps from the "original" functional space (2.5mm iso, same format as COPE images from FSL) to inflated FreeSurfer surfaces (created from 1.0mm MPRAGE image with recon-all pipeline) excluding voxels with a specific value (e.g. 0) from the averaging procedure of the projection. The reason for this is that I have non-continuous maps (i.e. map values are defined only for some voxels; voxels for which map value is not defined will have 0 as value). Is there a way to perform the projection excluding voxels with a specific value from the averaging of the projection? Thank you in advance for any help! Anna As complementary information: My maps have discrete values (between -10 and 10) and at the moment I am using the following command: mri_vol2surf --mov DiscreteMap.nii --reg $REGMAT --hemi lh --projfrac-avg 0 1 0.2 --interp nearest --o DiscreteMap _InFS_projAvg02_SurfLh.mgh However, in this way the resulting surface map will have values biased by including in the average also the 0 values which in reality represents voxels not included in the map. ___ 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] mri_vol2surf Averaging with exclusion of specific values
By default, the projection is done using nearest neighbor "interpolation", so there is no averaging. Is this what you mean? On 02/01/2016 09:53 AM, Gardumi Anna (PSYCHOLOGY) wrote: > > Dear FreeSurfer expert, > > I would like to project my maps from the “original” functional space > (2.5mm iso, same format as COPE images from FSL) to inflated > FreeSurfer surfaces (created from 1.0mm MPRAGE image with recon-all > pipeline) excluding voxels with a specific value (e.g. 0) from the > averaging procedure of the projection. The reason for this is that I > have non-continuous maps (i.e. map values are defined only for some > voxels; voxels for which map value is not defined will have 0 as > value). Is there a way to perform the projection excluding voxels with > a specific value from the averaging of the projection? > > Thank you in advance for any help! > > Anna > > As complementary information: > > My maps have discrete values (between -10 and 10) and at the moment I > am using the following command: > > mri_vol2surf --mov DiscreteMap.nii --reg $REGMAT --hemi lh > --projfrac-avg 0 1 0.2 --interp nearest --o DiscreteMap > _InFS_projAvg02_SurfLh.mgh > > However, in this way the resulting surface map will have values biased > by including in the average also the 0 values which in reality > represents voxels not included in the map. > > > > ___ > 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] matrix is ill-conditioned or badly scaled, condno = 27492.1
Try removing the mean from your covariate On 01/30/2016 01:31 PM, Nabin Koirala wrote: > Dear Freesurfer forum, > > 'I am trying to run qdec analysis for a group of subjects to see if > correlation exists but I am getting this error only for this > particular set of data but could not figure out what is exactly wrong > with it. Your suggestion would be greatly appreciated. > > Following is the terminal output for the process: > .. > Saving design matrix to /g/f/h/s/freesurfer/subjects/qdec/Untitled/Xg.dat > Normalized matrix condition is 27492.1 > Design matrix -- > 1.000 0.408; > 1.000 0.417; > 1.000 0.417; > 1.000 0.405; > 1.000 0.412; > 1.000 0.412; > 1.000 0.411; > 1.000 0.417; > 1.000 0.405; > 1.000 0.406; > 1.000 0.402; > 1.000 0.419; > 1.000 0.413; > 1.000 0.413; > > ERROR: matrix is ill-conditioned or badly scaled, condno = 27492.1 > > Possible problem with experimental design: > Check for duplicate entries and/or lack of range of > continuous variables within a class. > If you seek help with this problem, make sure to send: > 1. Your command line: > mri_glmfit --y /g/f/h/s/freesurfer/subjects/qdec/Untitled/y.mgh > --fsgd /g/f/h/s/freesurfer/subjects/qdec/Untitled/qdec.fsgd dods > --glmdir /g/f/h/s/freesurfer/subjects/qdec/Untitled --surf fsaverage > lh --label /g/f/h/s/freesurfer/subjects/fsaverage/label/lh.aparc.label > --C > /g/f/h/s/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat > > --C > /g/f/h/s/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-thickness-alpha1-Cor.mat > > > 2. The FSGD file (if using one) > 3. And the design matrix above > Error in Analyze: command failed: mri_glmfit --y > /g/f/h/s/freesurfer/subjects/qdec/Untitled/y.mgh --fsgd > /g/f/h/s/freesurfer/subjects/qdec/Untitled/qdec.fsgd dods --glmdir > /g/f/h/s/freesurfer/subjects/qdec/Untitled --surf fsaverage lh --label > /g/f/h/s/freesurfer/subjects/fsaverage/label/lh.aparc.label --C > /g/f/h/s/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat > > --C > /g/f/h/s/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-thickness-alpha1-Cor.mat > > Many thanks in advance. > > Regards, > Nabin > > > ___ > 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] mri_vol2surf Averaging with exclusion of specific values
Thank you for your reply. I am then a bit confused because I thought each surface value was the result of a two-step procedure: 1) sampling of the values along the normal to the surface at the points specified by the option --projfrac-avg min max del; with such values computed according the chosen interpolation method (nearest by default or specified by --interp nearest/trilinear); 2) averaging of the value obtained from point 1) Is this correct? What I would like is the following: 1) sampling along the normal at the nearest voxel to each point defined by --projfrac-avg min max del (I will obtain for example five values, let's say [1 0 1 2 2]) 2) averaging these values excluding from the mean points having a specific value (e.g. 0 so that I would obtain as a mean value 1.5, and not 1.2) I hope this clarify my point. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: maandag 1 februari 2016 17:14 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2surf Averaging with exclusion of specific values By default, the projection is done using nearest neighbor "interpolation", so there is no averaging. Is this what you mean? On 02/01/2016 09:53 AM, Gardumi Anna (PSYCHOLOGY) wrote: > > Dear FreeSurfer expert, > > I would like to project my maps from the "original" functional space > (2.5mm iso, same format as COPE images from FSL) to inflated > FreeSurfer surfaces (created from 1.0mm MPRAGE image with recon-all > pipeline) excluding voxels with a specific value (e.g. 0) from the > averaging procedure of the projection. The reason for this is that I > have non-continuous maps (i.e. map values are defined only for some > voxels; voxels for which map value is not defined will have 0 as > value). Is there a way to perform the projection excluding voxels with > a specific value from the averaging of the projection? > > Thank you in advance for any help! > > Anna > > As complementary information: > > My maps have discrete values (between -10 and 10) and at the moment I > am using the following command: > > mri_vol2surf --mov DiscreteMap.nii --reg $REGMAT --hemi lh > --projfrac-avg 0 1 0.2 --interp nearest --o DiscreteMap > _InFS_projAvg02_SurfLh.mgh > > However, in this way the resulting surface map will have values biased > by including in the average also the 0 values which in reality > represents voxels not included in the map. > > > > ___ > 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
[Freesurfer] Recon for Rhesus Macaque
Hello, I'm wondering what is the first step in reconstruction when working with rhesus macaque. script 01.05 requires files to be in mgh format initially ? I understand that the recon-all scipt is not setp to work with monkey data [cid:image003.jpg@01D15CF6.FFDB5710] Thanks, Rafael ___ 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] Recon for Rhesus Macaque
Thanks Sabastian! I received the new version of the scripts. So I can run 01.05 as the first step and just modify the locations and names of my files? Regards, Rafael -Original Message- From: Moeller, Sebastian [mailto:sebastian.moell...@rwth-aachen.de] Sent: Monday, February 01, 2016 2:56 PM To: Freesurfer support list Cc: Casas, Rafael (NIH/CC/DRD) [F] Subject: Re: [Freesurfer] Recon for Rhesus Macaque Hi Rafael, > On Feb 1, 2016, at 19:46 , Casas, Rafael (NIH/CC/DRD) [F] > wrote: > > Hello, > I’m wondering what is the first step in reconstruction when working with > rhesus macaque. script 01.05 requires files to be in mgh format initially ? One simple solution would be to either use mri_convert to convert the input volumes into mgh/mgz format, or just change the “set anat_name = mprage.mgz” line to reflec the actual format your files are in… (this requires a reasonably modern 01.05_average_anatomicals_mgz.csh though, not sure which version you are using over at NIH). Anyway I attached a recent enough version of the scripts, t this email, I do fear that they will not make it through the list server… ___ 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] Recon for Rhesus Macaque
Hi Rafael, > On Feb 1, 2016, at 21:18 , Casas, Rafael (NIH/CC/DRD) [F] > wrote: > > Thanks Sabastian! I received the new version of the scripts. > > So I can run 01.05 as the first step and just modify the locations and names > of my files? As you have not offered enough information about your exact setup/file formats I have no way of answering this question, sorry. You could start by reading the files I sent you and then just try it, though. For NHPs I would always start with making sure that the orientation information in the files really describes the anatomy of the animals, which typically are used in sphinx position, and only do all the rest after fixing this. Best Regards Sebastian > > Regards, > Rafael > > > > -Original Message- > From: Moeller, Sebastian [mailto:sebastian.moell...@rwth-aachen.de] > Sent: Monday, February 01, 2016 2:56 PM > To: Freesurfer support list > Cc: Casas, Rafael (NIH/CC/DRD) [F] > Subject: Re: [Freesurfer] Recon for Rhesus Macaque > > Hi Rafael, > > >> On Feb 1, 2016, at 19:46 , Casas, Rafael (NIH/CC/DRD) [F] >> wrote: >> >> Hello, >> I’m wondering what is the first step in reconstruction when working with >> rhesus macaque. script 01.05 requires files to be in mgh format initially ? > > One simple solution would be to either use mri_convert to convert the input > volumes into mgh/mgz format, or just change the “set anat_name = mprage.mgz” > line to reflec the actual format your files are in… (this requires a > reasonably modern 01.05_average_anatomicals_mgz.csh though, not sure which > version you are using over at NIH). > Anyway I attached a recent enough version of the scripts, t this email, > I do fear that they will not make it through the list server… ___ 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.
