[Freesurfer] fMRI activation color inversion
Hi FreeSurfer experts, I recently ran a simple fMRI analysis in FSL and now generating images of the activation in freesurfer using reg-feat2anat to register the functional activation to the freesurfer recon-all files, and generating the images using tksurfer: tksurfer pilot_3 lh inflated -annot aparc.annot -ov run4578_COMB.gfeat/cope1.feat/stats/zstat1.nii.gz -ovreg run4_fwhm8.feat/reg/freesurfer/anat2std.register.dat -fthresh 4 -fslope 1 However I have come across a strange occurrence when I change the threshold. Specifically, when I set the -fthresh flag (bolded) as 4 (i.e. p=0.0001) or less, the activation colors comes off as they should (see 4_blue attached) in terms of how I set up the contrasts. But when I set my threshold to 5 or higher (changing nothing else), the colors of the activation invert (see 5_red attached). What does this mean? How can I fix this? Any ideas would be greatly appreciated! Thank you! Gabriella Mass. Eye and Ear Confidentiality Notice: This e-mail and any files transmitted with it are confidential and are intended solely for the use of the individual(s) addressed in the message above. This communication may contain sensitive or confidential information. If you are not an intended recipient, dissemination, forwarding, printing, or copying of this e-mail is strictly prohibited. If you believe you have received this e-mail in error and the email contains patient information, please contact the Mass. Eye and Ear Compliance Line at 617-263-1600. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and delete 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 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] fMRI activation color inversion
Thanks Doug! This is very good to know. Is there a ratio or relationship between the fmin and fmax that is optimal, as in, should we keep a 2 to 5 ratio? Gabriella -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Monday, January 11, 2016 12:55 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fMRI activation color inversion There is another parameter called -fmid. The final mapping is a complicated combination of all three (fthresh, fmin, fslope). I usally use the -fminmax option which is easier to explain. -fminmax 2 5 means that the threshold is set to 2 and that at 5 the color will saturate. doug On 01/11/2016 12:18 PM, Hirsch, Gabriella wrote: > Hi FreeSurfer experts, > > I recently ran a simple fMRI analysis in FSL and now generating images > of the activation in freesurfer using reg-feat2anat to register the > functional activation to the freesurfer recon-all files, and > generating the images using tksurfer: > > /tksurfer pilot_3 lh inflated -annot aparc.annot -ov > run4578_COMB.gfeat/cope1.feat/stats/zstat1.nii.gz -ovreg > run4_fwhm8.feat/reg/freesurfer/anat2std.register.dat *-fthresh 4 > *-fslope 1/ > > However I have come across a strange occurrence when I change the > threshold. Specifically, when I set the -fthresh flag (bolded) as 4 > (i.e. p=0.0001) or less, the activation colors comes off as they > should (see 4_blue attached) in terms of how I set up the contrasts. > But when I set my threshold to 5 or higher (changing nothing else), > the colors of the activation invert (see 5_red attached). > > What does this mean? How can I fix this? > > Any ideas would be greatly appreciated! > > Thank you! > Gabriella > > > Mass. Eye and Ear Confidentiality Notice: This e-mail and any files > transmitted with it are confidential and are intended solely for the > use of the individual(s) addressed in the message above. This > communication may contain sensitive or confidential information. If > you are not an intended recipient, dissemination, forwarding, > printing, or copying of this e-mail is strictly prohibited. If you > believe you have received this e-mail in error and the email contains > patient information, please contact the Mass. Eye and Ear Compliance > Line at 617-263-1600. If the e-mail was sent to you in error but does > not contain patient information, please contact the sender and delete > the e-mail. > > > ___ > 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] fMRI activation color inversion
OK, thanks! Gabriella -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Monday, January 11, 2016 2:31 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fMRI activation color inversion no, it is a matter of taste. Note that 2 is the threshold. If you are looking at sig maps, then the threshold may be important. The p-value threshold is 10^-fthresh On 01/11/2016 02:19 PM, Hirsch, Gabriella wrote: > Thanks Doug! This is very good to know. Is there a ratio or relationship > between the fmin and fmax that is optimal, as in, should we keep a 2 to 5 > ratio? > > > Gabriella > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N > Greve > Sent: Monday, January 11, 2016 12:55 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] fMRI activation color inversion > > There is another parameter called -fmid. The final mapping is a complicated > combination of all three (fthresh, fmin, fslope). I usally use the -fminmax > option which is easier to explain. -fminmax 2 5 means that the threshold is > set to 2 and that at 5 the color will saturate. > doug > > On 01/11/2016 12:18 PM, Hirsch, Gabriella wrote: >> Hi FreeSurfer experts, >> >> I recently ran a simple fMRI analysis in FSL and now generating >> images of the activation in freesurfer using reg-feat2anat to >> register the functional activation to the freesurfer recon-all files, >> and generating the images using tksurfer: >> >> /tksurfer pilot_3 lh inflated -annot aparc.annot -ov >> run4578_COMB.gfeat/cope1.feat/stats/zstat1.nii.gz -ovreg >> run4_fwhm8.feat/reg/freesurfer/anat2std.register.dat *-fthresh 4 >> *-fslope 1/ >> >> However I have come across a strange occurrence when I change the >> threshold. Specifically, when I set the -fthresh flag (bolded) as 4 >> (i.e. p=0.0001) or less, the activation colors comes off as they >> should (see 4_blue attached) in terms of how I set up the contrasts. >> But when I set my threshold to 5 or higher (changing nothing else), >> the colors of the activation invert (see 5_red attached). >> >> What does this mean? How can I fix this? >> >> Any ideas would be greatly appreciated! >> >> Thank you! >> Gabriella >> >> >> Mass. Eye and Ear Confidentiality Notice: This e-mail and any files >> transmitted with it are confidential and are intended solely for the >> use of the individual(s) addressed in the message above. This >> communication may contain sensitive or confidential information. If >> you are not an intended recipient, dissemination, forwarding, >> printing, or copying of this e-mail is strictly prohibited. If you >> believe you have received this e-mail in error and the email contains >> patient information, please contact the Mass. Eye and Ear Compliance >> Line at 617-263-1600. If the e-mail was sent to you in error but does >> not contain patient information, please contact the sender and delete >> the e-mail. >> >> >> ___ >> 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 > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone N
[Freesurfer] modify QDEC smoothing options
Hey Freesurfer experts, I had a quick question. Is there any way to modify QDEC in such a way to have other options other than 0, 5, 10, 15, 20 etc, for smoothing? I know I would also have to -qcache the data for the desired smoothing too but I was wondering if anyone had done this before? Any ideas would be appreciated! Thanks, Gabriella * Confidentiality Notice: If you have received this e-mail in error, please immediately notify the sender by replying to this e-mail, keeping the original message intact. Please do not "Reply All." After replying to the sender, please delete this e-mail from your files. Information contained in this e-mail is only for the use of the individual(s) or entity for whom it is intended, even if addressed incorrectly. ___ 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] qdec analysis with ICV
Hi Freesurfer Experts, I am hoping someone can help me solve this error I'm experiencing while conducting a simple qdec analysis. I have 4 subjects (3 vs 1) that I am trying to analyze for volume differences using a demeaned ICV as a nuisance factor (see attached fsgd file - note I changed the .dat extension as my email server didn't like the dat format). However, I am getting this error: Normalized matrix condition is 1e+08 Design matrix -- 0.000 1.000 0.000 -28915.199; 0.000 1.000 0.000 194736.703; 0.000 1.000 0.000 -184311.000; 1.000 0.000 18489.000 0.000; ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 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 /media/seagate_external_/freesurfer_subjects/qdec/Untitled/y.mgh --fsgd /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd dods --glmdir /media/seagate_external_/freesurfer_subjects/qdec/Untitled --surf fsaverage rh --label /media/seagate_external_/freesurfer_subjects/fsaverage/label/rh.aparc.label --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-volume-ICV-Cor.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Cor-volume-ICV.mat 2. The FSGD file (if using one) 3. And the design matrix above Error in Analyze: command failed: mri_glmfit --y /media/seagate_external_/freesurfer_subjects/qdec/Untitled/y.mgh --fsgd /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd dods --glmdir /media/seagate_external_/freesurfer_subjects/qdec/Untitled --surf fsaverage rh --label /media/seagate_external_/freesurfer_subjects/fsaverage/label/rh.aparc.label --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-volume-ICV-Cor.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Cor-volume-ICV.mat There are no duplicate entries. I have done this same analysis with a higher number of subjects without problems. I have also tried using the inbuilt qdec ICV (which is not demeaned) and got the same error. Could this be a problem with the small subject count? If so, is there any way to remedy it? Thank you! Gabriella * Confidentiality Notice: If you have received this e-mail in error, please immediately notify the sender by replying to this e-mail, keeping the original message intact. Please do not "Reply All." After replying to the sender, please delete this e-mail from your files. Information contained in this e-mail is only for the use of the individual(s) or entity for whom it is intended, even if addressed incorrectly. fsid group ICV FLS_08212014 PVL -28915.2 MWB_07252014 PVL 194736.7 MMJ_06142013 PVL -184311 FEK_11172014 CVI 18489 ___ 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] qdec analysis with ICV
Thanks for the suggestion David. I tried it but I still got the same error :/ Gabriella From: David Vazquez [mailto:dvazq...@ucr.edu] Sent: Friday, November 13, 2015 12:36 PM To: Hirsch, Gabriella Subject: Re: [Freesurfer] qdec analysis with ICV Hi Gabriella. I'm not an expert, but I've had this problem too. Reduce the number of digits for ICV by converting it be cm^3 instead of mm^3. Also get rid of some decimal places. It works for us. Good luck. -David On Fri, Nov 13, 2015, 8:10 AM Hirsch, Gabriella <gabriella_hir...@meei.harvard.edu<mailto:gabriella_hir...@meei.harvard.edu>> wrote: Hi Freesurfer Experts, I am hoping someone can help me solve this error I'm experiencing while conducting a simple qdec analysis. I have 4 subjects (3 vs 1) that I am trying to analyze for volume differences using a demeaned ICV as a nuisance factor (see attached fsgd file - note I changed the .dat extension as my email server didn't like the dat format). However, I am getting this error: Normalized matrix condition is 1e+08 Design matrix -- 0.000 1.000 0.000 -28915.199; 0.000 1.000 0.000 194736.703; 0.000 1.000 0.000 -184311.000; 1.000 0.000 18489.000 0.000; ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 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 /media/seagate_external_/freesurfer_subjects/qdec/Untitled/y.mgh --fsgd /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd dods --glmdir /media/seagate_external_/freesurfer_subjects/qdec/Untitled --surf fsaverage rh --label /media/seagate_external_/freesurfer_subjects/fsaverage/label/rh.aparc.label --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-volume-ICV-Cor.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Cor-volume-ICV.mat 2. The FSGD file (if using one) 3. And the design matrix above Error in Analyze: command failed: mri_glmfit --y /media/seagate_external_/freesurfer_subjects/qdec/Untitled/y.mgh --fsgd /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd dods --glmdir /media/seagate_external_/freesurfer_subjects/qdec/Untitled --surf fsaverage rh --label /media/seagate_external_/freesurfer_subjects/fsaverage/label/rh.aparc.label --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-volume-ICV-Cor.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Cor-volume-ICV.mat There are no duplicate entries. I have done this same analysis with a higher number of subjects without problems. I have also tried using the inbuilt qdec ICV (which is not demeaned) and got the same error. Could this be a problem with the small subject count? If so, is there any way to remedy it? Thank you! Gabriella • Confidentiality Notice: If you have received this e-mail in error, please immediately notify the sender by replying to this e-mail, keeping the original message intact. Please do not “Reply All.” After replying to the sender, please delete this e-mail from your files. Information contained in this e-mail is only for the use of the individual(s) or entity for whom it is intended, even if addressed incorrectly. ___ Freesurfer mailing list 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. • Confidentiality Notice: If you have received this e-mail in error, please immediately notify the sender by replying to this e-mail, keeping the original message intact. Please do not “Reply All.” After replying to the sender, please delete this e-mail from your files. Information contained in this e-mail is only for the use of the individual(s) or entity for whom it is intended, even if add
Re: [Freesurfer] qdec analysis with ICV
Hi Andrew, the values I'm using are already mean centered -- similarly, I've never been able to use the full ICV values. Even with David's suggestion of reducing the number of digits (effectively making the numbers smaller), it still doesn't work... Gabriella From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of O'Shea,Andrew Sent: Friday, November 13, 2015 1:55 PM To: freesurfer@nmr.mgh.harvard.edu; David Vazquez Subject: Re: [Freesurfer] qdec analysis with ICV Try mean centering your ICV values (I.e. Subtract the mean value from each individual value). This has worked for me to bypass this error. -Andrew From: <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of "Hirsch, Gabriella" <gabriella_hir...@meei.harvard.edu<mailto:gabriella_hir...@meei.harvard.edu>> Reply-To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Friday, November 13, 2015 at 1:03 PM To: David Vazquez <dvazq...@ucr.edu<mailto:dvazq...@ucr.edu>> Cc: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] qdec analysis with ICV Thanks for the suggestion David. I tried it but I still got the same error :/ Gabriella From: David Vazquez [mailto:dvazq...@ucr.edu] Sent: Friday, November 13, 2015 12:36 PM To: Hirsch, Gabriella Subject: Re: [Freesurfer] qdec analysis with ICV Hi Gabriella. I'm not an expert, but I've had this problem too. Reduce the number of digits for ICV by converting it be cm^3 instead of mm^3. Also get rid of some decimal places. It works for us. Good luck. -David On Fri, Nov 13, 2015, 8:10 AM Hirsch, Gabriella <gabriella_hir...@meei.harvard.edu<mailto:gabriella_hir...@meei.harvard.edu>> wrote: Hi Freesurfer Experts, I am hoping someone can help me solve this error I'm experiencing while conducting a simple qdec analysis. I have 4 subjects (3 vs 1) that I am trying to analyze for volume differences using a demeaned ICV as a nuisance factor (see attached fsgd file - note I changed the .dat extension as my email server didn't like the dat format). However, I am getting this error: Normalized matrix condition is 1e+08 Design matrix -- 0.000 1.000 0.000 -28915.199; 0.000 1.000 0.000 194736.703; 0.000 1.000 0.000 -184311.000; 1.000 0.000 18489.000 0.000; ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 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 /media/seagate_external_/freesurfer_subjects/qdec/Untitled/y.mgh --fsgd /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd dods --glmdir /media/seagate_external_/freesurfer_subjects/qdec/Untitled --surf fsaverage rh --label /media/seagate_external_/freesurfer_subjects/fsaverage/label/rh.aparc.label --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-volume-ICV-Cor.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Cor-volume-ICV.mat 2. The FSGD file (if using one) 3. And the design matrix above Error in Analyze: command failed: mri_glmfit --y /media/seagate_external_/freesurfer_subjects/qdec/Untitled/y.mgh --fsgd /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd dods --glmdir /media/seagate_external_/freesurfer_subjects/qdec/Untitled --surf fsaverage rh --label /media/seagate_external_/freesurfer_subjects/fsaverage/label/rh.aparc.label --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-volume-ICV-Cor.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Cor-volume-ICV.mat There are no duplicate entries. I have done this same analysis with a higher number of subjects without problems. I have also tried using the inbuilt qdec ICV (which is not demeaned) and got the same error. Could this be a problem with the small subject count? If so, is there any way to remedy it? Thank you! Gabriella * Confidential
Re: [Freesurfer] qdec analysis with ICV
That does make sense Andrew. But would that be the case even if I weren't correcting for ICV? In other words, the analysis works when I don't correct for it. The GLM still looks for variance in group differences regardless if you're correcting for something or not...right? From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of O'Shea,Andrew Sent: Friday, November 13, 2015 4:07 PM To: Freesurfer support list Subject: Re: [Freesurfer] qdec analysis with ICV I believe your issue is you are trying to do a between group analysis but you only have 1 subject in group B. There is no way to estimate the variance in the measure if there is only one subject in the group. -Andrew From: <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of "Hirsch, Gabriella" <gabriella_hir...@meei.harvard.edu<mailto:gabriella_hir...@meei.harvard.edu>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Friday, November 13, 2015 at 1:58 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] qdec analysis with ICV Hi Andrew, the values I'm using are already mean centered -- similarly, I've never been able to use the full ICV values. Even with David's suggestion of reducing the number of digits (effectively making the numbers smaller), it still doesn't work... Gabriella From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of O'Shea,Andrew Sent: Friday, November 13, 2015 1:55 PM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>; David Vazquez Subject: Re: [Freesurfer] qdec analysis with ICV Try mean centering your ICV values (I.e. Subtract the mean value from each individual value). This has worked for me to bypass this error. -Andrew From: <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of "Hirsch, Gabriella" <gabriella_hir...@meei.harvard.edu<mailto:gabriella_hir...@meei.harvard.edu>> Reply-To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Friday, November 13, 2015 at 1:03 PM To: David Vazquez <dvazq...@ucr.edu<mailto:dvazq...@ucr.edu>> Cc: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] qdec analysis with ICV Thanks for the suggestion David. I tried it but I still got the same error :/ Gabriella From: David Vazquez [mailto:dvazq...@ucr.edu] Sent: Friday, November 13, 2015 12:36 PM To: Hirsch, Gabriella Subject: Re: [Freesurfer] qdec analysis with ICV Hi Gabriella. I'm not an expert, but I've had this problem too. Reduce the number of digits for ICV by converting it be cm^3 instead of mm^3. Also get rid of some decimal places. It works for us. Good luck. -David On Fri, Nov 13, 2015, 8:10 AM Hirsch, Gabriella <gabriella_hir...@meei.harvard.edu<mailto:gabriella_hir...@meei.harvard.edu>> wrote: Hi Freesurfer Experts, I am hoping someone can help me solve this error I'm experiencing while conducting a simple qdec analysis. I have 4 subjects (3 vs 1) that I am trying to analyze for volume differences using a demeaned ICV as a nuisance factor (see attached fsgd file - note I changed the .dat extension as my email server didn't like the dat format). However, I am getting this error: Normalized matrix condition is 1e+08 Design matrix -- 0.000 1.000 0.000 -28915.199; 0.000 1.000 0.000 194736.703; 0.000 1.000 0.000 -184311.000; 1.000 0.000 18489.000 0.000; ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 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 /media/seagate_external_/freesurfer_subjects/qdec/Untitled/y.mgh --fsgd /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd dods --glmdir /media/seagate_external_/freesurfer_subjects/qdec/Untitled --surf fsaverage rh --label /media/seagate_external_/freesurfer_subjects/fsaverage/label/rh.aparc.label --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-volume-ICV-Cor.mat --C /media/seagate_e
Re: [Freesurfer] create ROI from label
Ah, running into a slight snag. I placed the new version in the freesurfer/bin folder but I'm running into permission issues: /usr/local/freesurfer/bin/mri_label2vol: Permission denied. Tried chmod-ing it but still didn't work: chmod +x mri_label2vol chmod: changing permissions of `mri_label2vol': Operation not permitted Am I missing something? Thanks, Gabriella 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, September 08, 2015 2:35 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] create ROI from label try this version ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol On 09/08/2015 02:30 PM, Hirsch, Gabriella wrote: > Thanks Doug - I tried adding it but got an error: > > ERROR: Option --fill-ribbon unknown > > Does the order matter/should some other flag be removed? > > Thanks, > Gabriella > > 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, September 08, 2015 1:10 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] create ROI from label > > Try it with --fill-ribbon > > On 09/08/2015 11:01 AM, Hirsch, Gabriella wrote: >> Hi all, >> >> I'm trying to generate an ROI mask from the Freesurfer label >> lh.MT.label of a specific subject. I've browsed the documentation and >> the archives and it seems the best command to use is mri_label2vol. >> However, I can only seem to produce the "outline" of the label, if >> that makes sense (as when you load the label on an inflated brain in >> tksurfer). >> >> Is there any way to create a 3D "filled in" ROI in .nii format to then >> use in FSL, for instance? I tried playing around with the values in >> the --fillthresh and --proj flags but no dice. >> >> Here is the command I've been using: >> >> *mri_label2vol --label $SUBJECTS_DIR/*MBZ_07102015*/label/lh.MT.label >> --label$SUBJECTS_DIR/*MBZ_07102015/label/lh.MT.label --temp >> $*SUBJECTS_DIR/*MBZ_07102015/mri/T1.mgz --reg* >> $SUBJECTS_DIR/*MBZ_07102015/stats/register.dat* *--fillthresh 0 --o* >> $*SUBJECTS_DIR**/MBZ_07102015/new_lh.MT.nii.gz >> Any suggestions would be greatly appreciated! >> >> Thanks, >> Gabriella >> >> >> ___ >> 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 > > -- 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] create ROI from label
Hi all, I'm trying to generate an ROI mask from the Freesurfer label lh.MT.label of a specific subject. I've browsed the documentation and the archives and it seems the best command to use is mri_label2vol. However, I can only seem to produce the "outline" of the label, if that makes sense (as when you load the label on an inflated brain in tksurfer). Is there any way to create a 3D "filled in" ROI in .nii format to then use in FSL, for instance? I tried playing around with the values in the --fillthresh and --proj flags but no dice. Here is the command I've been using: mri_label2vol --label $SUBJECTS_DIR/MBZ_07102015/label/lh.MT.label --label $SUBJECTS_DIR/MBZ_07102015/label/lh.MT.label --temp $SUBJECTS_DIR/MBZ_07102015/mri/T1.mgz --reg $SUBJECTS_DIR/MBZ_07102015/stats/register.dat --fillthresh 0 --o $SUBJECTS_DIR/MBZ_07102015/new_lh.MT.nii.gz Any suggestions would be greatly appreciated! Thanks, Gabriella ___ 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] create ROI from label
Thanks Doug - I tried adding it but got an error: ERROR: Option --fill-ribbon unknown Does the order matter/should some other flag be removed? Thanks, Gabriella 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, September 08, 2015 1:10 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] create ROI from label Try it with --fill-ribbon On 09/08/2015 11:01 AM, Hirsch, Gabriella wrote: > Hi all, > > I'm trying to generate an ROI mask from the Freesurfer label > lh.MT.label of a specific subject. I've browsed the documentation and > the archives and it seems the best command to use is mri_label2vol. > However, I can only seem to produce the "outline" of the label, if > that makes sense (as when you load the label on an inflated brain in > tksurfer). > > Is there any way to create a 3D "filled in" ROI in .nii format to then > use in FSL, for instance? I tried playing around with the values in > the --fillthresh and --proj flags but no dice. > > Here is the command I've been using: > > *mri_label2vol --label $SUBJECTS_DIR/*MBZ_07102015*/label/lh.MT.label > --label$SUBJECTS_DIR/*MBZ_07102015/label/lh.MT.label --temp > $*SUBJECTS_DIR/*MBZ_07102015/mri/T1.mgz --reg* > $SUBJECTS_DIR/*MBZ_07102015/stats/register.dat* *--fillthresh 0 --o* > $*SUBJECTS_DIR**/MBZ_07102015/new_lh.MT.nii.gz > Any suggestions would be greatly appreciated! > > Thanks, > Gabriella > > > ___ > 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] feat statistics on surface
Hi Freesurfer experts, I am still trying to resolve the problem detailed below. It seems my version of reg-feat2anat is not working properly since it does not created the anat2exf.register.dat file needed to view fmri data analysed with FSL on the subjects native surface in FS. Doug posted a new version in response to a user about a year ago, but this seems to have been deleted/moved: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/reg-feat2anat Does someone know where I can update to this new version? Thank you! Gabriella From: Hirsch, Gabriella Sent: Monday, June 22, 2015 4:53 PM To: freesurfer@nmr.mgh.harvard.edu Subject: reg-feat2anat update Hi FS experts, I had a quick query I was hoping you could help with; I am trying to load functional data analyzed in FSL in Freesurfer using reg-feat2anat (http://freesurfer.net/fswiki/FsTutorial/RegisterFeatOntoAnatomical) and seem to be having the same problem as the person in this thread: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-June/038639.htmlhttps://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-June/038639.html In other words, the anat2exf.register.dat file is not being created. I tried to download the new version of reg-feat2anat posted by Doug in the thread but I'm getting an error when downloading with wget: no such file reg-feat2anat Has the location of this file changed? Thank you! Best, Gabriella ___ 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] FW: reg-feat2anat update
Hi FS experts, Sorry for re-posting, but I never heard back and would love to get this working! Any ideas on why my download didn't work or if there is a new location of the new reg-feat2anat version? Thank you! Gabriella From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Hirsch, Gabriella Sent: Monday, June 22, 2015 4:53 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] reg-feat2anat update Hi FS experts, I had a quick query I was hoping you could help with; I am trying to load functional data analyzed in FSL in Freesurfer using reg-feat2anat (http://freesurfer.net/fswiki/FsTutorial/RegisterFeatOntoAnatomical) and seem to be having the same problem as the person in this thread: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-June/038639.htmlhttps://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-June/038639.html In other words, the anat2exf.register.dat file is not being created. I tried to download the new version of reg-feat2anat posted by Doug in the thread but I'm getting an error when downloading with wget: no such file reg-feat2anat Has the location of this file changed? Thank you! Best, Gabriella ___ 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] reg-feat2anat update
Hi FS experts, I had a quick query I was hoping you could help with; I am trying to load functional data analyzed in FSL in Freesurfer using reg-feat2anat (http://freesurfer.net/fswiki/FsTutorial/RegisterFeatOntoAnatomical) and seem to be having the same problem as the person in this thread: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-June/038639.html In other words, the anat2exf.register.dat file is not being created. I tried to download the new version of reg-feat2anat posted by Doug in the thread but I'm getting an error when downloading with wget: no such file reg-feat2anat Has the location of this file changed? Thank you! Best, Gabriella ___ 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] FW: correcting for brain size
I was actually looking for total area.pial surface..? Sorry, I forget FS calls it area.pial while area is wm. Is there a way to find this value? Gabriella -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Thursday, May 28, 2015 2:20 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size isn't that what you are looking for? On 05/28/2015 02:05 PM, Hirsch, Gabriella wrote: Hmm, I tried looking and all I can find is total wm surface area and surface area of individual regions. I've attached an lh.aparc.stats file for one of the subjects. Am I missing something? Thanks so much! 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: Thursday, May 28, 2015 1:37 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size It is actually in ?h.aparc.stats. The total is the total for the hemi On 05/28/2015 09:12 AM, Hirsch, Gabriella wrote: That's what I thought but it doesn't seem to be there; I only have the following: BrainSegVol BrainSegVolNotVent BrainSegVolNotVentSurf lhCortexVol rhCortexVol CortexVol lhCorticalWhiteMatterVol rhCorticalWhiteMatterVol CorticalWhiteMatterVol SubCortGrayVol TotalGrayVol SupraTentorialVol SupraTentorialVolNotVent SupraTentorialVolNotVentVox MaskVol BrainSegVol-to-eTIV MaskVol-to-eTIV lhSurfaceHoles rhSurfaceHoles SurfaceHoles eTIV Is there a way to create it? Thanks! 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: Wednesday, May 27, 2015 6:12 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size There should be one in aseg.stats. On 05/27/2015 05:45 PM, Hirsch, Gabriella wrote: Yes, it seems to be a qdec issue since mri_glmfit works by itself even without demeaning the larger values of ICV. Thanks anyway. One unrelated questions since I have you here; does FS produce a total or global cortical surface area file along the lines of TotalGrayVol? I'm looking for the best measure to correct during a group surface area analysis. Thanks again for all your help. Gabriella -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Wednesday, May 27, 2015 5:40 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Oh, sorry, this is not a problem with mri_glmfit as I had thought. It is a problem with qdec itself on your data. I'm not sure what to tell you because I can't debug it without your data (and maybe not even then). You can use mri_glmfit directly. doug On 05/27/2015 04:49 PM, Hirsch, Gabriella wrote: Done. I wasn't sure if I had to put an email address for the recipient so I put yours. Let me know if you figure it out! :) Thanks so much. Gabriella -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Wednesday, May 27, 2015 4:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Hmm, still can't replicate the error. Can you post this file to our filedrop (see end of msg for url) /media/seagate_external_/freesurfer_subjects/qdec/Untitled/y.mgh On 05/27/2015 04:40 PM, Hirsch, Gabriella wrote: Sure. 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: Wednesday, May 27, 2015 4:35 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size still not sure, can you send these files? /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contras ts/ lh-Avg-Intercept-thickness.mat /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contras ts/ l h-Diff-EB-control-Intercept-thickness.mat On 05/27/2015 04:30 PM, Hirsch, Gabriella wrote: Sure thing, see attached. 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: Wednesday, May 27, 2015 4:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Can you send me /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.f sgd On 05/27/2015 03:47 PM, Hirsch, Gabriella wrote: Thanks for the response, Doug! Yes, here is the error message I get when I try
Re: [Freesurfer] FW: correcting for brain size
Hmm, I tried looking and all I can find is total wm surface area and surface area of individual regions. I've attached an lh.aparc.stats file for one of the subjects. Am I missing something? Thanks so much! 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: Thursday, May 28, 2015 1:37 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size It is actually in ?h.aparc.stats. The total is the total for the hemi On 05/28/2015 09:12 AM, Hirsch, Gabriella wrote: That's what I thought but it doesn't seem to be there; I only have the following: BrainSegVol BrainSegVolNotVent BrainSegVolNotVentSurf lhCortexVol rhCortexVol CortexVol lhCorticalWhiteMatterVol rhCorticalWhiteMatterVol CorticalWhiteMatterVol SubCortGrayVol TotalGrayVol SupraTentorialVol SupraTentorialVolNotVent SupraTentorialVolNotVentVox MaskVol BrainSegVol-to-eTIV MaskVol-to-eTIV lhSurfaceHoles rhSurfaceHoles SurfaceHoles eTIV Is there a way to create it? Thanks! 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: Wednesday, May 27, 2015 6:12 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size There should be one in aseg.stats. On 05/27/2015 05:45 PM, Hirsch, Gabriella wrote: Yes, it seems to be a qdec issue since mri_glmfit works by itself even without demeaning the larger values of ICV. Thanks anyway. One unrelated questions since I have you here; does FS produce a total or global cortical surface area file along the lines of TotalGrayVol? I'm looking for the best measure to correct during a group surface area analysis. Thanks again for all your help. Gabriella -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Wednesday, May 27, 2015 5:40 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Oh, sorry, this is not a problem with mri_glmfit as I had thought. It is a problem with qdec itself on your data. I'm not sure what to tell you because I can't debug it without your data (and maybe not even then). You can use mri_glmfit directly. doug On 05/27/2015 04:49 PM, Hirsch, Gabriella wrote: Done. I wasn't sure if I had to put an email address for the recipient so I put yours. Let me know if you figure it out! :) Thanks so much. Gabriella -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Wednesday, May 27, 2015 4:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Hmm, still can't replicate the error. Can you post this file to our filedrop (see end of msg for url) /media/seagate_external_/freesurfer_subjects/qdec/Untitled/y.mgh On 05/27/2015 04:40 PM, Hirsch, Gabriella wrote: Sure. 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: Wednesday, May 27, 2015 4:35 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size still not sure, can you send these files? /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/ lh-Avg-Intercept-thickness.mat /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/ l h-Diff-EB-control-Intercept-thickness.mat On 05/27/2015 04:30 PM, Hirsch, Gabriella wrote: Sure thing, see attached. 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: Wednesday, May 27, 2015 4:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Can you send me /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd On 05/27/2015 03:47 PM, Hirsch, Gabriella wrote: Thanks for the response, Doug! Yes, here is the error message I get when I try to keep one measure (e.g. ICV or global volume) in QDEC. As I said earlier, when I keep BOTH measures (like keeping both ICV and global volume as nuisance factors) in a simple thickness analysis between two groups, then the analysis is successful. If I only keep one, then QDEC simply closes automatically and I get the attached error. I kept everything qdec outputted for completeness in the attached .txt file. Interestingly, when I run mri_glmfit manually in the terminal, I can pose one measure (e.g global volume) as a covariate without
Re: [Freesurfer] FW: correcting for brain size
Yes, it seems to be a qdec issue since mri_glmfit works by itself even without demeaning the larger values of ICV. Thanks anyway. One unrelated questions since I have you here; does FS produce a total or global cortical surface area file along the lines of TotalGrayVol? I'm looking for the best measure to correct during a group surface area analysis. Thanks again for all your help. Gabriella -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Wednesday, May 27, 2015 5:40 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Oh, sorry, this is not a problem with mri_glmfit as I had thought. It is a problem with qdec itself on your data. I'm not sure what to tell you because I can't debug it without your data (and maybe not even then). You can use mri_glmfit directly. doug On 05/27/2015 04:49 PM, Hirsch, Gabriella wrote: Done. I wasn't sure if I had to put an email address for the recipient so I put yours. Let me know if you figure it out! :) Thanks so much. Gabriella -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Wednesday, May 27, 2015 4:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Hmm, still can't replicate the error. Can you post this file to our filedrop (see end of msg for url) /media/seagate_external_/freesurfer_subjects/qdec/Untitled/y.mgh On 05/27/2015 04:40 PM, Hirsch, Gabriella wrote: Sure. 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: Wednesday, May 27, 2015 4:35 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size still not sure, can you send these files? /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/ lh-Avg-Intercept-thickness.mat /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/ l h-Diff-EB-control-Intercept-thickness.mat On 05/27/2015 04:30 PM, Hirsch, Gabriella wrote: Sure thing, see attached. 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: Wednesday, May 27, 2015 4:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Can you send me /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd On 05/27/2015 03:47 PM, Hirsch, Gabriella wrote: Thanks for the response, Doug! Yes, here is the error message I get when I try to keep one measure (e.g. ICV or global volume) in QDEC. As I said earlier, when I keep BOTH measures (like keeping both ICV and global volume as nuisance factors) in a simple thickness analysis between two groups, then the analysis is successful. If I only keep one, then QDEC simply closes automatically and I get the attached error. I kept everything qdec outputted for completeness in the attached .txt file. Interestingly, when I run mri_glmfit manually in the terminal, I can pose one measure (e.g global volume) as a covariate without demeaning and the analysis seemingly works (I don't get any errors, anyway). Thank you! Gabriella 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: Wednesday, May 27, 2015 3:23 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Hi Gabriella, sorry for the delay On 05/22/2015 09:15 AM, Hirsch, Gabriella wrote: HI FS experts, I haven't heard back and am still wrestling with these questions. Any takers? I'd really appreciate any thoughts at all if possible. Thanks, Gabriella *From:*Hirsch, Gabriella *Sent:* Wednesday, May 20, 2015 3:55 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* ICV correction for volume analysis Hi FreeSurfer experts, I have a couple quick questions I'm hoping someone can clarify for me; I am conducting a group surface-based morphometry analysis in all three measures in 2 groups (patient and control) and am looking for the best way to correct for brain size variability in the cortical volume analysis. My question is: 1.So far, I've been using Qdec, however qdec seems to crash when I ask it to pose ICV as a nuisance factor. In the archives, we are told to mean center the ICV values in order for Qdec to take it, but I was informed that mean centering was not a good idea in morphometry studies. Any thoughts? It may or may not be a problem depending on what you are doing. I prefer
Re: [Freesurfer] FW: correcting for brain size
Sure. 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: Wednesday, May 27, 2015 4:35 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size still not sure, can you send these files? /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/lh-Diff-EB-control-Intercept-thickness.mat On 05/27/2015 04:30 PM, Hirsch, Gabriella wrote: Sure thing, see attached. 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: Wednesday, May 27, 2015 4:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Can you send me /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd On 05/27/2015 03:47 PM, Hirsch, Gabriella wrote: Thanks for the response, Doug! Yes, here is the error message I get when I try to keep one measure (e.g. ICV or global volume) in QDEC. As I said earlier, when I keep BOTH measures (like keeping both ICV and global volume as nuisance factors) in a simple thickness analysis between two groups, then the analysis is successful. If I only keep one, then QDEC simply closes automatically and I get the attached error. I kept everything qdec outputted for completeness in the attached .txt file. Interestingly, when I run mri_glmfit manually in the terminal, I can pose one measure (e.g global volume) as a covariate without demeaning and the analysis seemingly works (I don't get any errors, anyway). Thank you! Gabriella 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: Wednesday, May 27, 2015 3:23 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Hi Gabriella, sorry for the delay On 05/22/2015 09:15 AM, Hirsch, Gabriella wrote: HI FS experts, I haven’t heard back and am still wrestling with these questions. Any takers? I’d really appreciate any thoughts at all if possible. Thanks, Gabriella *From:*Hirsch, Gabriella *Sent:* Wednesday, May 20, 2015 3:55 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* ICV correction for volume analysis Hi FreeSurfer experts, I have a couple quick questions I’m hoping someone can clarify for me; I am conducting a group surface-based morphometry analysis in all three measures in 2 groups (patient and control) and am looking for the best way to correct for brain size variability in the cortical volume analysis. My question is: 1.So far, I’ve been using Qdec, however qdec seems to crash when I ask it to pose ICV as a nuisance factor. In the archives, we are told to “mean center” the ICV values in order for Qdec to take it, but I was informed that mean centering was not a good idea in morphometry studies. Any thoughts? It may or may not be a problem depending on what you are doing. I prefer to divide the glm input value by the ICV, but some like to use as a regressor. If you want to do it that way, then you'll have to demean, or you might try to just scale all ICVs to bring them into a range similar to that of the input value. 2.I’ve found that in QDEC, if I include ICV AND global mean volume as nuisance factors, the analysis works. If I only include ONE of the two variables, it crashes. This is super frustrating – is there any way around this issue? Saying that it crashes is not too informative. Can you give more info? Eg, an error message? 3.If I want to keep only the raw ICV values in my analysis (i.e. not demean it), what’s the best way to go about this? Do I have to re-run the analysis using mri_glmfit with the ICV values as a covariate in my fsgd file (with a contrast like 1 -1 0 0, with age and ICV as covariates)? I tried doing it this way and got some questionable results. I want to make sure I’m executing this correctly. You can scale the input or scale the ICV as I mention above. You can also run it as a DOSS (different offset, same slope) doug I’d really appreciate any help on this. Thank you! Gabriella ___ 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
Re: [Freesurfer] FW: correcting for brain size
Done. I wasn't sure if I had to put an email address for the recipient so I put yours. Let me know if you figure it out! :) Thanks so much. Gabriella -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Wednesday, May 27, 2015 4:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Hmm, still can't replicate the error. Can you post this file to our filedrop (see end of msg for url) /media/seagate_external_/freesurfer_subjects/qdec/Untitled/y.mgh On 05/27/2015 04:40 PM, Hirsch, Gabriella wrote: Sure. 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: Wednesday, May 27, 2015 4:35 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size still not sure, can you send these files? /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/l h-Diff-EB-control-Intercept-thickness.mat On 05/27/2015 04:30 PM, Hirsch, Gabriella wrote: Sure thing, see attached. 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: Wednesday, May 27, 2015 4:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Can you send me /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd On 05/27/2015 03:47 PM, Hirsch, Gabriella wrote: Thanks for the response, Doug! Yes, here is the error message I get when I try to keep one measure (e.g. ICV or global volume) in QDEC. As I said earlier, when I keep BOTH measures (like keeping both ICV and global volume as nuisance factors) in a simple thickness analysis between two groups, then the analysis is successful. If I only keep one, then QDEC simply closes automatically and I get the attached error. I kept everything qdec outputted for completeness in the attached .txt file. Interestingly, when I run mri_glmfit manually in the terminal, I can pose one measure (e.g global volume) as a covariate without demeaning and the analysis seemingly works (I don't get any errors, anyway). Thank you! Gabriella 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: Wednesday, May 27, 2015 3:23 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Hi Gabriella, sorry for the delay On 05/22/2015 09:15 AM, Hirsch, Gabriella wrote: HI FS experts, I haven't heard back and am still wrestling with these questions. Any takers? I'd really appreciate any thoughts at all if possible. Thanks, Gabriella *From:*Hirsch, Gabriella *Sent:* Wednesday, May 20, 2015 3:55 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* ICV correction for volume analysis Hi FreeSurfer experts, I have a couple quick questions I'm hoping someone can clarify for me; I am conducting a group surface-based morphometry analysis in all three measures in 2 groups (patient and control) and am looking for the best way to correct for brain size variability in the cortical volume analysis. My question is: 1.So far, I've been using Qdec, however qdec seems to crash when I ask it to pose ICV as a nuisance factor. In the archives, we are told to mean center the ICV values in order for Qdec to take it, but I was informed that mean centering was not a good idea in morphometry studies. Any thoughts? It may or may not be a problem depending on what you are doing. I prefer to divide the glm input value by the ICV, but some like to use as a regressor. If you want to do it that way, then you'll have to demean, or you might try to just scale all ICVs to bring them into a range similar to that of the input value. 2.I've found that in QDEC, if I include ICV AND global mean volume as nuisance factors, the analysis works. If I only include ONE of the two variables, it crashes. This is super frustrating - is there any way around this issue? Saying that it crashes is not too informative. Can you give more info? Eg, an error message? 3.If I want to keep only the raw ICV values in my analysis (i.e. not demean it), what's the best way to go about this? Do I have to re-run the analysis using mri_glmfit with the ICV values as a covariate in my fsgd file (with a contrast like 1 -1 0 0, with age and ICV as covariates)? I tried doing it this way and got some questionable results. I want to make sure I'm executing this correctly. You can scale
Re: [Freesurfer] FW: correcting for brain size
Sure thing, see attached. 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: Wednesday, May 27, 2015 4:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Can you send me /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd On 05/27/2015 03:47 PM, Hirsch, Gabriella wrote: Thanks for the response, Doug! Yes, here is the error message I get when I try to keep one measure (e.g. ICV or global volume) in QDEC. As I said earlier, when I keep BOTH measures (like keeping both ICV and global volume as nuisance factors) in a simple thickness analysis between two groups, then the analysis is successful. If I only keep one, then QDEC simply closes automatically and I get the attached error. I kept everything qdec outputted for completeness in the attached .txt file. Interestingly, when I run mri_glmfit manually in the terminal, I can pose one measure (e.g global volume) as a covariate without demeaning and the analysis seemingly works (I don't get any errors, anyway). Thank you! Gabriella 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: Wednesday, May 27, 2015 3:23 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Hi Gabriella, sorry for the delay On 05/22/2015 09:15 AM, Hirsch, Gabriella wrote: HI FS experts, I haven’t heard back and am still wrestling with these questions. Any takers? I’d really appreciate any thoughts at all if possible. Thanks, Gabriella *From:*Hirsch, Gabriella *Sent:* Wednesday, May 20, 2015 3:55 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* ICV correction for volume analysis Hi FreeSurfer experts, I have a couple quick questions I’m hoping someone can clarify for me; I am conducting a group surface-based morphometry analysis in all three measures in 2 groups (patient and control) and am looking for the best way to correct for brain size variability in the cortical volume analysis. My question is: 1.So far, I’ve been using Qdec, however qdec seems to crash when I ask it to pose ICV as a nuisance factor. In the archives, we are told to “mean center” the ICV values in order for Qdec to take it, but I was informed that mean centering was not a good idea in morphometry studies. Any thoughts? It may or may not be a problem depending on what you are doing. I prefer to divide the glm input value by the ICV, but some like to use as a regressor. If you want to do it that way, then you'll have to demean, or you might try to just scale all ICVs to bring them into a range similar to that of the input value. 2.I’ve found that in QDEC, if I include ICV AND global mean volume as nuisance factors, the analysis works. If I only include ONE of the two variables, it crashes. This is super frustrating – is there any way around this issue? Saying that it crashes is not too informative. Can you give more info? Eg, an error message? 3.If I want to keep only the raw ICV values in my analysis (i.e. not demean it), what’s the best way to go about this? Do I have to re-run the analysis using mri_glmfit with the ICV values as a covariate in my fsgd file (with a contrast like 1 -1 0 0, with age and ICV as covariates)? I tried doing it this way and got some questionable results. I want to make sure I’m executing this correctly. You can scale the input or scale the ICV as I mention above. You can also run it as a DOSS (different offset, same slope) doug I’d really appreciate any help on this. Thank you! Gabriella ___ 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] FW: correcting for brain size
Thanks David! Gabriella From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of David Vazquez Sent: Friday, May 22, 2015 6:19 PM To: Freesurfer support list Subject: Re: [Freesurfer] FW: correcting for brain size Hi Gabriella, I'm not an expert in freesurfer. I've worked with freesurfer for 5 years now. When we started I had the same problem when including ICV in the qdec table and running it as a nuisance variable. I'm assuming you have ICV in mm^3. Try converting it to cm^3 or dcm^3 in your qdec table. That worked for us. I think qdec might have a problem with numbers in the millions/hundred thousands. Just don't forget to reconvert when you are interpreting/writing your results or else it can get confusing. Maybe its just us, but when we use ICV as a covariate many, many significant clusters were diminished to nothing. Hope this helps. -David Vazquez PhD candidate in Cognitive Neuroscience University of California, Riverside NSF GRFP fellow On Fri, May 22, 2015 at 6:16 AM Hirsch, Gabriella gabriella_hir...@meei.harvard.edumailto:gabriella_hir...@meei.harvard.edu wrote: HI FS experts, I haven’t heard back and am still wrestling with these questions. Any takers? I’d really appreciate any thoughts at all if possible. Thanks, Gabriella From: Hirsch, Gabriella Sent: Wednesday, May 20, 2015 3:55 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: ICV correction for volume analysis Hi FreeSurfer experts, I have a couple quick questions I’m hoping someone can clarify for me; I am conducting a group surface-based morphometry analysis in all three measures in 2 groups (patient and control) and am looking for the best way to correct for brain size variability in the cortical volume analysis. My question is: 1. So far, I’ve been using Qdec, however qdec seems to crash when I ask it to pose ICV as a nuisance factor. In the archives, we are told to “mean center” the ICV values in order for Qdec to take it, but I was informed that mean centering was not a good idea in morphometry studies. Any thoughts? 2. I’ve found that in QDEC, if I include ICV AND global mean volume as nuisance factors, the analysis works. If I only include ONE of the two variables, it crashes. This is super frustrating – is there any way around this issue? 3. If I want to keep only the raw ICV values in my analysis (i.e. not demean it), what’s the best way to go about this? Do I have to re-run the analysis using mri_glmfit with the ICV values as a covariate in my fsgd file (with a contrast like 1 -1 0 0, with age and ICV as covariates)? I tried doing it this way and got some questionable results. I want to make sure I’m executing this correctly. I’d really appreciate any help on this. Thank you! Gabriella ___ 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 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] FW: correcting for brain size
HI FS experts, I haven't heard back and am still wrestling with these questions. Any takers? I'd really appreciate any thoughts at all if possible. Thanks, Gabriella From: Hirsch, Gabriella Sent: Wednesday, May 20, 2015 3:55 PM To: freesurfer@nmr.mgh.harvard.edu Subject: ICV correction for volume analysis Hi FreeSurfer experts, I have a couple quick questions I'm hoping someone can clarify for me; I am conducting a group surface-based morphometry analysis in all three measures in 2 groups (patient and control) and am looking for the best way to correct for brain size variability in the cortical volume analysis. My question is: 1. So far, I've been using Qdec, however qdec seems to crash when I ask it to pose ICV as a nuisance factor. In the archives, we are told to mean center the ICV values in order for Qdec to take it, but I was informed that mean centering was not a good idea in morphometry studies. Any thoughts? 2. I've found that in QDEC, if I include ICV AND global mean volume as nuisance factors, the analysis works. If I only include ONE of the two variables, it crashes. This is super frustrating - is there any way around this issue? 3. If I want to keep only the raw ICV values in my analysis (i.e. not demean it), what's the best way to go about this? Do I have to re-run the analysis using mri_glmfit with the ICV values as a covariate in my fsgd file (with a contrast like 1 -1 0 0, with age and ICV as covariates)? I tried doing it this way and got some questionable results. I want to make sure I'm executing this correctly. I'd really appreciate any help on this. Thank you! Gabriella ___ 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] ICV correction for volume analysis
Hi FreeSurfer experts, I have a couple quick questions I'm hoping someone can clarify for me; I am conducting a group surface-based morphometry analysis in all three measures in 2 groups (patient and control) and am looking for the best way to correct for brain size variability in the cortical volume analysis. Based on my particular experiment, it seems estimated ICV (or eTIV) found in the /subject/stats/aseg.stats file would be sufficient. My question is: 1. So far, I've been using Qdec, however qdec seems to crash when I ask it to pose ICV as a nuisance factor. In the archives, we are told to mean center the ICV values in order for Qdec to take it, but I was informed that mean centering was not a good idea in morphometry studies. Any thoughts? 2. If I want to keep the raw ICV values in my analysis (i.e. not demean it), what's the best way to go about this? Do I have to re-run the analysis using mri_glmfit with the ICV values as a covariate in my fsgd file (with a contrast like 1 -1 0 0, with age and ICV as covariates)? I'd really appreciate any help on this. Thank you! Gabriella ___ 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] demean values in QDEC
Hi FS experts, I had a quick silly question about QDEC - I'm trying to run a group morphometry analysis of cortical volume between two groups (patient and control). I want to use ICV as a nuisance covariate and noticed you need to demean the ICV values in order for QDEC to work. My question is: Is there a way to demean these values within QDEC? Or do I have to manually demean these and then add them as a covariate to my qdec.table.dat? Thank you! Gabriella ___ 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] qdec table loading error
Scratch that - I simply changed the level name from blind to EB and it worked. Clearly qdec didn't like my naming assignments. Thanks anyway! Gabriella From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Hirsch, Gabriella Sent: Thursday, May 07, 2015 3:02 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] qdec table loading error Hi FS experts, I'm having a really tough time trying to get my qdec.table.dat table to load into the qdec GUI. I have gone through the wiki painstakingly and have no idea why it's giving me this error message: Reading /usr/local/freesurfer/tktools/tkUtils.tcl Using /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Loading data table /media/seagate_external_/freesurfer_subjects/qdec/qdec.table.dat... Number of columns: 2 fsid column:1 Number of factors: 1 Number of subjects: 18 Reading discrete factor levels from config file /media/seagate_external_/freesurfer_subjects/qdec/group.levels control blind done. ERROR: Subject FLY_03072013 has an invalid level 'blind' in the group column INFO: If 'group' is a discrete factor, then create a file named 'group.levels' containing the valid factor names one per line. Error loading the data table. For the record, I definitely have a group.levels file in my qdec directory with the two levels (blind and control) of the discrete factor (group). Any ideas? Thank you! Gabriella ___ 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] qdec table loading error
Hi FS experts, I'm having a really tough time trying to get my qdec.table.dat table to load into the qdec GUI. I have gone through the wiki painstakingly and have no idea why it's giving me this error message: Reading /usr/local/freesurfer/tktools/tkUtils.tcl Using /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Loading data table /media/seagate_external_/freesurfer_subjects/qdec/qdec.table.dat... Number of columns: 2 fsid column:1 Number of factors: 1 Number of subjects: 18 Reading discrete factor levels from config file /media/seagate_external_/freesurfer_subjects/qdec/group.levels control blind done. ERROR: Subject FLY_03072013 has an invalid level 'blind' in the group column INFO: If 'group' is a discrete factor, then create a file named 'group.levels' containing the valid factor names one per line. Error loading the data table. For the record, I definitely have a group.levels file in my qdec directory with the two levels (blind and control) of the discrete factor (group). Any ideas? Thank you! Gabriella ___ 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] interpreting glmfit-sim results
Hello FS experts, I submitted this question yesterday but never heard back. Any thoughts? Thank you! Gabriella From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Hirsch, Gabriella Sent: Monday, May 04, 2015 3:03 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] interpreting glmfit-sim results Hi FS experts, I had a couple quick questions about interpreting glmfit-sim results. For context, I'm interesting in analyzing surface-based morphology differences (cortical thickness, volume, surface area) between two groups. I ran a simple t-test contrast (1 -1) using glmfit on two groups (control and patient) and then corrected for multiple comparisons with glmfit-sim using mc-z. My question is 1) I assume this is a two-tailed t-test (I used absolute in the clusterwise correction)? And 2) Is there a place where the direction of the results is easily readable (other than visualizing the cluster colors)? Apologies if this is trivial - I couldn't find anything in the archive. Thanks! Gabriella ___ 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] interpreting glmfit-sim results
Hi FS experts, I had a couple quick questions about interpreting glmfit-sim results. For context, I'm interesting in analyzing surface-based morphology differences (cortical thickness, volume, surface area) between two groups. I ran a simple t-test contrast (1 -1) using glmfit on two groups (control and patient) and then corrected for multiple comparisons with glmfit-sim using mc-z. My question is 1) I assume this is a two-tailed t-test (I used absolute in the clusterwise correction)? And 2) Is there a place where the direction of the results is easily readable (other than visualizing the cluster colors)? Apologies if this is trivial - I couldn't find anything in the archive. Thanks! Gabriella ___ 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] glmfit-sim question
Hi FS experts, I had a quick question about glmfit-sim in monte carlo. I have followed the FS wiki by using the following command to correct for multiple comparisons separately on both hemispheres: mri_glmfit-sim \ --glmdir_?h.xxx.glmdir \ --sim mc-z 1 1.3 mc-z.absolute \ --sim-sign abs --cwpvalthresh 0.05 \ --overwrite However I've been reading the mail archive and it seems it is necessary to do a bonferroni correction on both hemispheres as well. My questions are: 1.I can add the --2spaces flag at the end even though I'm using FS v5.3? 2. If not, do I have to change my cwpvalthresh (i.e. to 0.025) or do I need to change the -log10(p) value in the third line? Any help would be appreciated. P.S FYI I'm running a simple group analysis on two groups (1 group 2 levels, using a 1 -1 contrast). Thanks! Gabriella ___ 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] tksurfer overlay threshold
Hi Zeke and Bruce. Thanks for catching the type. Though, I'm still getting the invalid command name error Gabriella -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Wednesday, March 04, 2015 11:53 AM To: Z K Cc: Freesurfer support list Subject: Re: [Freesurfer] tksurfer overlay threshold oh, thanks Zeke for catching that Bruce On Wed, 4 Mar 2015, Z K wrote: Hi Gabriela, You might have a typo. Its set_current_threshold_from_percentile not set_threshold_from_percentile as you have in your email. -Zeke On 03/04/2015 11:07 AM, Bruce Fischl wrote: you would need to include parameters, but that doesn't explain your error. What version of tksurfer are you using? It is probably too old On Wed, 4 Mar 2015, Hirsch, Gabriella wrote: Hi Bruce, I tried using the command set_threshold_from_percentile as a tcl script but I got the following error: tksurfer: run tcl script: threshold.tcl invalid command name set_threshold_from_percentile% Do I have to add values to the tcl command as well? From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, March 04, 2015 10:26 AM To: Freesurfer support list Subject: Re: [Freesurfer] tksurfer overlay threshold Hi Gabriela they set the threshold so that 92% of the values are not displayed, and the color scale saturates at the 99 percentile cheers Bruce On Wed, 4 Mar 2015, Hirsch, Gabriella wrote: Thanks Bruce! I tried using the command: sclv_set_current_threshold_from_percentile The tried using the values .92, .925, .99 as noted on the wiki but I'm still not quite sure what these percentages do in terms of setting the threshold? Thanks! Gabriella -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, March 03, 2015 7:05 PM To: Freesurfer support list Subject: Re: [Freesurfer] tksurfer overlay threshold you can use the command: set_current_threshold_from_percentile(min, mid,max) which will compute the thresholds based on the histogram of values On Tue, 3 Mar 2015, Douglas N Greve wrote: I'm not sure what you mean. optimal in what sense? doug On 03/03/2015 03:21 PM, Hirsch, Gabriella wrote: Hi Fs experts, I had a quick question about settings thresholds of surface overlays in Tksurfer. I am currently generating images of the thickness, volume and surface area of individual subjects, and would like to know if there are optimal minimum and maximum threshold values to be set for different surfaces. For example, when overlaying thickness (from /surf/?h.thickness), I have set the min threshold to 1 or 1.3 (see attached); however I'm not sure this same threshold holds up in the other surfaces (e.g. surface area). In summary, is there an optimal way to determine what this min. and max. threshold should be in function of the distribution displayed in the threshold window (see attached, on the left)? Thank you! Gabriella ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tksurfer overlay threshold
I'm using freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 I'm not sure how to check the version of tksurfer specifically? From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, March 04, 2015 11:07 AM To: Freesurfer support list Subject: Re: [Freesurfer] tksurfer overlay threshold you would need to include parameters, but that doesn't explain your error. What version of tksurfer are you using? It is probably too old On Wed, 4 Mar 2015, Hirsch, Gabriella wrote: Hi Bruce, I tried using the command set_threshold_from_percentile as a tcl script but I got the following error: tksurfer: run tcl script: threshold.tcl invalid command name set_threshold_from_percentile% Do I have to add values to the tcl command as well? From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, March 04, 2015 10:26 AM To: Freesurfer support list Subject: Re: [Freesurfer] tksurfer overlay threshold Hi Gabriela they set the threshold so that 92% of the values are not displayed, and the color scale saturates at the 99 percentile cheers Bruce On Wed, 4 Mar 2015, Hirsch, Gabriella wrote: Thanks Bruce! I tried using the command: sclv_set_current_threshold_from_percentile The tried using the values .92, .925, .99 as noted on the wiki but I'm still not quite sure what these percentages do in terms of setting the threshold? Thanks! Gabriella -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, March 03, 2015 7:05 PM To: Freesurfer support list Subject: Re: [Freesurfer] tksurfer overlay threshold you can use the command: set_current_threshold_from_percentile(min, mid,max) which will compute the thresholds based on the histogram of values On Tue, 3 Mar 2015, Douglas N Greve wrote: I'm not sure what you mean. optimal in what sense? doug On 03/03/2015 03:21 PM, Hirsch, Gabriella wrote: Hi Fs experts, I had a quick question about settings thresholds of surface overlays in Tksurfer. I am currently generating images of the thickness, volume and surface area of individual subjects, and would like to know if there are optimal minimum and maximum threshold values to be set for different surfaces. For example, when overlaying thickness (from /surf/?h.thickness), I have set the min threshold to 1 or 1.3 (see attached); however I'm not sure this same threshold holds up in the other surfaces (e.g. surface area). In summary, is there an optimal way to determine what this min. and max. threshold should be in function of the distribution displayed in the threshold window (see attached, on the left)? Thank you! Gabriella ___ 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 ___ 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
Re: [Freesurfer] tksurfer overlay threshold
OK, I tried that, and it does load however I get this message in the terminal: tksurfer: run tcl script: threshold.tcl Wrong # args: sclv_set_current_threshold_from_percentile thresh mid slope% Also, the threshold continues to be the same as the default Thanks! Gabriella From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, March 04, 2015 4:07 PM To: Freesurfer support list Subject: Re: [Freesurfer] tksurfer overlay threshold try: sclv_set_current_threshold_from_percentile cheers Bruce On Wed, 4 Mar 2015, Hirsch, Gabriella wrote: Hi Bruce, I have been in touch with Zeke, who was kind enough to help me update my version of Tksurfer. Unfortunately, this has not solved my problem (see below). I am attaching here my command prompts in case I have missed anything; tksurfer subject rh inflated -overlay /media/seagate_external/freesurfer_subjects/subject/surf/rh.thickness -tcl threshold.tcl in the threshold.tcl I added the command: set_current_threshold_from_percentile When I run it, tksurfer loads my surface and overlay, but I receive the following message in the terminal: tksurfer: run tcl script: threshold.tcl invalid command name set_current_threshold_from_percentile% Any thoughts would be greatly appreciated! Thank you. Gabriella From: Z K [zkauf...@nmr.mgh.harvard.edu] Sent: Wednesday, March 04, 2015 2:32 PM To: Hirsch, Gabriella Subject: Re: [Freesurfer] tksurfer overlay threshold Yeah I figured that would be the case. Your best bet in this situation is to respond to Bruce's last email on the Freesurfer list and say that Zeke provided you with the most recent version of tksurfer but the command still does not work. You may want to copy/paste your exact command and terminal output so that he's sure this isnt a typo thing or some other small mistake. Sorry but that is the best I can do. I have no idea how to diagnose or solve the issue you are encountering. -Zeke On 03/04/2015 02:00 PM, Hirsch, Gabriella wrote: oops! sorry. Well, good news, tksurfer is installed and now runs. bad news, I'm still getting the error message: tksurfer: run tcl script: threshold.tcl invalid command name set_current_threshold_from_percentile% From: Z K [zkauf...@nmr.mgh.harvard.edu] Sent: Wednesday, March 04, 2015 1:49 PM To: Hirsch, Gabriella Subject: Re: [Freesurfer] tksurfer overlay threshold You'll need to make it executable. Type the following commands in the terminal window: $ cd $FREESURFER_HOME/tktools $ chmod a+x tksurfer* and let me know how it goes. -Zeke On 03/04/2015 01:38 PM, Hirsch, Gabriella wrote: Still having issues calling it up - I noticed the tksurfer.bin is labeled as an unknown file type as opposed to program like tkmedit.bin. Might this be the reason it isn't being recognized? Gabriella -Original Message- From: Z K [mailto:zkauf...@nmr.mgh.harvard.edu] Sent: Wednesday, March 04, 2015 12:55 PM To: Hirsch, Gabriella Subject: Re: [Freesurfer] tksurfer overlay threshold Perhaps there was a miscommunication. I gave you a tksurfer.bin file which was supposed to replace the tksurfer.bin you already had. The one you already had should be renamed to tksurfer.bin.orig for backup purposes. This time lets just do a complete reinstall of tksurfer. Please download the following 3 files: ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/tksurfer ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/tksurfer.bin ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/tksurfer.tcl And place them into your $FREESURFER_HOME/tktools directory. Be sure the executable bit is set but that should already be the case: $ cd $FREESURFER_HOME/tktools $ chmod a+x tksurfer* Now try again. Unfortunaly the more I look at this the more I doubt it is going to resolve the *set_current_threshold* issue, but its still worth a shot. -Zeke On 03/04/2015 12:39 PM, Hirsch, Gabriella wrote: We've run into a slight problem. I downloaded and replaced the old tksurfer with the new one, but now it's not recognizing it. It just says command not found when I call tksurfer. Is it perhaps a permissions issue? Gabriella -Original Message- From: Z K [mailto:zkauf...@nmr.mgh.harvard.edu] Sent: Wednesday, March 04, 2015 12:10 PM To: Hirsch, Gabriella Cc: Bruce Fischl Subject: Re: [Freesurfer] tksurfer overlay threshold Hi Gabriela, Im providing you with the most recent version of tksurfer. I have only slim hopes this will solve the issue for you, but its worth a shot. Please download the following file: ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries
Re: [Freesurfer] tksurfer overlay threshold
Hi Bruce, I have been in touch with Zeke, who was kind enough to help me update my version of Tksurfer. Unfortunately, this has not solved my problem (see below). I am attaching here my command prompts in case I have missed anything; tksurfer subject rh inflated -overlay /media/seagate_external/freesurfer_subjects/subject/surf/rh.thickness -tcl threshold.tcl in the threshold.tcl I added the command: set_current_threshold_from_percentile When I run it, tksurfer loads my surface and overlay, but I receive the following message in the terminal: tksurfer: run tcl script: threshold.tcl invalid command name set_current_threshold_from_percentile% Any thoughts would be greatly appreciated! Thank you. Gabriella From: Z K [zkauf...@nmr.mgh.harvard.edu] Sent: Wednesday, March 04, 2015 2:32 PM To: Hirsch, Gabriella Subject: Re: [Freesurfer] tksurfer overlay threshold Yeah I figured that would be the case. Your best bet in this situation is to respond to Bruce's last email on the Freesurfer list and say that Zeke provided you with the most recent version of tksurfer but the command still does not work. You may want to copy/paste your exact command and terminal output so that he's sure this isnt a typo thing or some other small mistake. Sorry but that is the best I can do. I have no idea how to diagnose or solve the issue you are encountering. -Zeke On 03/04/2015 02:00 PM, Hirsch, Gabriella wrote: oops! sorry. Well, good news, tksurfer is installed and now runs. bad news, I'm still getting the error message: tksurfer: run tcl script: threshold.tcl invalid command name set_current_threshold_from_percentile% From: Z K [zkauf...@nmr.mgh.harvard.edu] Sent: Wednesday, March 04, 2015 1:49 PM To: Hirsch, Gabriella Subject: Re: [Freesurfer] tksurfer overlay threshold You'll need to make it executable. Type the following commands in the terminal window: $ cd $FREESURFER_HOME/tktools $ chmod a+x tksurfer* and let me know how it goes. -Zeke On 03/04/2015 01:38 PM, Hirsch, Gabriella wrote: Still having issues calling it up - I noticed the tksurfer.bin is labeled as an unknown file type as opposed to program like tkmedit.bin. Might this be the reason it isn't being recognized? Gabriella -Original Message- From: Z K [mailto:zkauf...@nmr.mgh.harvard.edu] Sent: Wednesday, March 04, 2015 12:55 PM To: Hirsch, Gabriella Subject: Re: [Freesurfer] tksurfer overlay threshold Perhaps there was a miscommunication. I gave you a tksurfer.bin file which was supposed to replace the tksurfer.bin you already had. The one you already had should be renamed to tksurfer.bin.orig for backup purposes. This time lets just do a complete reinstall of tksurfer. Please download the following 3 files: ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/tksurfer ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/tksurfer.bin ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/tksurfer.tcl And place them into your $FREESURFER_HOME/tktools directory. Be sure the executable bit is set but that should already be the case: $ cd $FREESURFER_HOME/tktools $ chmod a+x tksurfer* Now try again. Unfortunaly the more I look at this the more I doubt it is going to resolve the *set_current_threshold* issue, but its still worth a shot. -Zeke On 03/04/2015 12:39 PM, Hirsch, Gabriella wrote: We've run into a slight problem. I downloaded and replaced the old tksurfer with the new one, but now it's not recognizing it. It just says command not found when I call tksurfer. Is it perhaps a permissions issue? Gabriella -Original Message- From: Z K [mailto:zkauf...@nmr.mgh.harvard.edu] Sent: Wednesday, March 04, 2015 12:10 PM To: Hirsch, Gabriella Cc: Bruce Fischl Subject: Re: [Freesurfer] tksurfer overlay threshold Hi Gabriela, Im providing you with the most recent version of tksurfer. I have only slim hopes this will solve the issue for you, but its worth a shot. Please download the following file: ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/cen tos6_x86_64/tksurfer.bin And place it into your $FREESURFER_HOME/tktools directory. Backup the version you already have there by renaming to tksurfer.bin.orig. Please let us know if this solves your issue or not. -Zeke On 03/04/2015 11:27 AM, Bruce Fischl wrote: Zeke: can you get Gabriela a current version of tksurfer and the associated tcl scripts? thanks Bruce On Wed, 4 Mar 2015, Hirsch, Gabriella wrote: I'm using freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 I'm not sure how to check the version of tksurfer specifically? From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce
Re: [Freesurfer] tksurfer overlay threshold
It works. I will play with this a bit. Thank you! Gabriella -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Wednesday, March 04, 2015 4:42 PM To: Freesurfer support list Subject: Re: [Freesurfer] tksurfer overlay threshold you need it to be: % sclv_set_current_threshold_from_percentile .7 .8 .9 or something like taht On Wed, 4 Mar 2015, Hirsch, Gabriella wrote: OK, I tried that, and it does load however I get this message in the terminal: tksurfer: run tcl script: threshold.tcl Wrong # args: sclv_set_current_threshold_from_percentile thresh mid slope% Also, the threshold continues to be the same as the default Thanks! Gabriella From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, March 04, 2015 4:07 PM To: Freesurfer support list Subject: Re: [Freesurfer] tksurfer overlay threshold try: sclv_set_current_threshold_from_percentile cheers Bruce On Wed, 4 Mar 2015, Hirsch, Gabriella wrote: Hi Bruce, I have been in touch with Zeke, who was kind enough to help me update my version of Tksurfer. Unfortunately, this has not solved my problem (see below). I am attaching here my command prompts in case I have missed anything; tksurfer subject rh inflated -overlay /media/seagate_external/freesurfer_subjects/subject/surf/rh.thickness -tcl threshold.tcl in the threshold.tcl I added the command: set_current_threshold_from_percentile When I run it, tksurfer loads my surface and overlay, but I receive the following message in the terminal: tksurfer: run tcl script: threshold.tcl invalid command name set_current_threshold_from_percentile% Any thoughts would be greatly appreciated! Thank you. Gabriella From: Z K [zkauf...@nmr.mgh.harvard.edu] Sent: Wednesday, March 04, 2015 2:32 PM To: Hirsch, Gabriella Subject: Re: [Freesurfer] tksurfer overlay threshold Yeah I figured that would be the case. Your best bet in this situation is to respond to Bruce's last email on the Freesurfer list and say that Zeke provided you with the most recent version of tksurfer but the command still does not work. You may want to copy/paste your exact command and terminal output so that he's sure this isnt a typo thing or some other small mistake. Sorry but that is the best I can do. I have no idea how to diagnose or solve the issue you are encountering. -Zeke On 03/04/2015 02:00 PM, Hirsch, Gabriella wrote: oops! sorry. Well, good news, tksurfer is installed and now runs. bad news, I'm still getting the error message: tksurfer: run tcl script: threshold.tcl invalid command name set_current_threshold_from_percentile% From: Z K [zkauf...@nmr.mgh.harvard.edu] Sent: Wednesday, March 04, 2015 1:49 PM To: Hirsch, Gabriella Subject: Re: [Freesurfer] tksurfer overlay threshold You'll need to make it executable. Type the following commands in the terminal window: $ cd $FREESURFER_HOME/tktools $ chmod a+x tksurfer* and let me know how it goes. -Zeke On 03/04/2015 01:38 PM, Hirsch, Gabriella wrote: Still having issues calling it up - I noticed the tksurfer.bin is labeled as an unknown file type as opposed to program like tkmedit.bin. Might this be the reason it isn't being recognized? Gabriella -Original Message- From: Z K [mailto:zkauf...@nmr.mgh.harvard.edu] Sent: Wednesday, March 04, 2015 12:55 PM To: Hirsch, Gabriella Subject: Re: [Freesurfer] tksurfer overlay threshold Perhaps there was a miscommunication. I gave you a tksurfer.bin file which was supposed to replace the tksurfer.bin you already had. The one you already had should be renamed to tksurfer.bin.orig for backup purposes. This time lets just do a complete reinstall of tksurfer. Please download the following 3 files: ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/ centos6_x86_64/tksurfer ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/ centos6_x86_64/tksurfer.bin ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/ centos6_x86_64/tksurfer.tcl And place them into your $FREESURFER_HOME/tktools directory. Be sure the executable bit is set but that should already be the case: $ cd $FREESURFER_HOME/tktools $ chmod a+x tksurfer* Now try again. Unfortunaly the more I look at this the more I doubt it is going to resolve the *set_current_threshold* issue, but its still worth a shot. -Zeke On 03/04/2015 12:39 PM, Hirsch, Gabriella wrote: We've run into a slight problem. I downloaded and replaced the old tksurfer with the new one, but now it's not recognizing it. It just says command not found when I call tksurfer. Is it perhaps
Re: [Freesurfer] tksurfer overlay threshold
I'm just trying to figure out what the min. and max. threshold should be in function of the distribution in order to obtain the most accurate representation of the overlay data in the visualizer. Any thoughts? Thanks! Gabriella -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Tuesday, March 03, 2015 5:48 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] tksurfer overlay threshold I'm not sure what you mean. optimal in what sense? doug On 03/03/2015 03:21 PM, Hirsch, Gabriella wrote: Hi Fs experts, I had a quick question about settings thresholds of surface overlays in Tksurfer. I am currently generating images of the thickness, volume and surface area of individual subjects, and would like to know if there are optimal minimum and maximum threshold values to be set for different surfaces. For example, when overlaying thickness (from /surf/?h.thickness), I have set the min threshold to 1 or 1.3 (see attached); however I'm not sure this same threshold holds up in the other surfaces (e.g. surface area). In summary, is there an optimal way to determine what this min. and max. threshold should be in function of the distribution displayed in the threshold window (see attached, on the left)? Thank you! Gabriella ___ 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] tksurfer overlay threshold
Thanks Bruce! I tried using the command: sclv_set_current_threshold_from_percentile The tried using the values .92, .925, .99 as noted on the wiki but I'm still not quite sure what these percentages do in terms of setting the threshold? Thanks! Gabriella -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, March 03, 2015 7:05 PM To: Freesurfer support list Subject: Re: [Freesurfer] tksurfer overlay threshold you can use the command: set_current_threshold_from_percentile(min, mid,max) which will compute the thresholds based on the histogram of values On Tue, 3 Mar 2015, Douglas N Greve wrote: I'm not sure what you mean. optimal in what sense? doug On 03/03/2015 03:21 PM, Hirsch, Gabriella wrote: Hi Fs experts, I had a quick question about settings thresholds of surface overlays in Tksurfer. I am currently generating images of the thickness, volume and surface area of individual subjects, and would like to know if there are optimal minimum and maximum threshold values to be set for different surfaces. For example, when overlaying thickness (from /surf/?h.thickness), I have set the min threshold to 1 or 1.3 (see attached); however I'm not sure this same threshold holds up in the other surfaces (e.g. surface area). In summary, is there an optimal way to determine what this min. and max. threshold should be in function of the distribution displayed in the threshold window (see attached, on the left)? Thank you! Gabriella ___ 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
Re: [Freesurfer] cluster colors
Yes - sorry this is probably easier with images. The files I'm visualizing are the sig.mgh (uncorrected) and cache.th13.abs.sig.ocn. mgh (cluster corrected) respectively, overlayed on an fsaverage brain. I am visualizing using tksurfer. When I run mri_glmfit, I get the example_sig output (see attached), which was expected. However, after I run the clusterwise correction (mri_glmfit-sim), my clusters come out in a different color (in this case red, every time, for every cluster; see example_cluster). The tutorial indicates the cluster color scale is arbitrary, however, ALL of my clusters post-correction are always the same color, and always different from the pre-corrected clusters. I found this a little confusing since red is a color from the heat map, which may be interpreted as an inverse of the original uncorrected output - but it seems this color is in fact arbitrary. Is this correct? Gabriella From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve Sent: Wednesday, February 18, 2015 2:16 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] cluster colors I don't think I understand. What files are you visualizing? What is your command to visualize? On 2/18/15 3:42 PM, Hirsch, Gabriella wrote: Hi FS experts, I had a quick question I was hoping someone could help me with; I used the group analysis tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis_tktools) to analyse two groups of subjects. I ran the mri_glmfit command, as well as the clusterwise correction (mri_glmfit-sim) on the same data; however upon visualization, the two outputs present clusters in different colors (before correction all clusters are blue and after post-correction all clusters are red - this is consistent across conditions). According to the tutorial, I should disregard the red color since it is arbitrary (and not, in fact, an inversion of what I see from the uncorrected data). Note that I have NOT changed the contrast or any other setting. Am I understanding this correctly? Thank you. Gabriella ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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] cluster colors
Hi FS experts, I had a quick question I was hoping someone could help me with; I used the group analysis tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis_tktools) to analyse two groups of subjects. I ran the mri_glmfit command, as well as the clusterwise correction (mri_glmfit-sim) on the same data; however upon visualization, the two outputs present clusters in different colors (before correction all clusters are blue and after post-correction all clusters are red - this is consistent across conditions). According to the tutorial, I should disregard the red color since it is arbitrary (and not, in fact, an inversion of what I see from the uncorrected data). Note that I have NOT changed the contrast or any other setting. Am I understanding this correctly? Thank you. Gabriella ___ 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] group analysis question
Hi FS experts, I sent a similar question to this last week but I never got a response. Any ideas would be very much appreciated! I have gone through the Group Analysis tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisDng) and am trying to find a way to extract uncorrected significance values. I saw there is a way to do this using the clusterwise correction steps (i.e. via the cluster summary text file), but I was wondering if you knew a way of obtaining extracting the p-values prior to correcting. I'm assuming these values would be embedded in the sig.mgh file since this what is used as an overlay in the visualizer? Do you have any suggestions? I'd really appreciate any ideas. Thanks so much! Best, Gabriella ___ 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] extracting pvalues
Hi FreeSurfer experts, Is there a way to extract significant pvalues from sig.mgh files (Obtained from the GroupAnalysisDng tutorial)? I've looked online but having trouble. Somehow mris_covert isn't working. Thanks! Gabriella ___ 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] cortical thickness analysis
Hi freesurfer experts, I have a question I was hoping someone could help me with; I am currently analysing the cortical thickness of two subject populations (patient and control) using the group analysis tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisDng). However, when I ran the processing stream for the clusterwise correction for multiple comparisons, all my visualized clusters all disappeared (using tksurfer or freeview) and no clusters showed to be significant in the CWP column of the cluster summary txt file (NClusters=0). I have played around with the thresholds but it doesn't seem to make much of a difference. For what it's worth, I'm using a simple t-test contrast. Any thoughts as to what is going on? Similarly, is there any way of accessing p-values of uncorrected clusters? Thanks so much for your help. Best, Gabriella ___ 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 analysis freeview error
Hello, I have encountered a silly error message I'm hoping someone can help me with. I've been following the GLM analysis tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis) and have managed to go through all the steps; however I am now having issues visualizing my results. Having called the command: freeview -f $SUBJECTS_DIR/fsaverage/surf/ lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.control_CVI.glmdir/contrast/sig.mgh:overlay_threshold=4,5 -viewport 3d I get the error: Unrecognized sub-option flag 'annot_outline'. Any ideas on what this might be? I appreciate your help. Thanks! Gabriella ___ 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] qdec group analysis error
Hello there, I am trying to run an analysis in qdec with 25 subjects, 1 factor (diagnosis) with three levels (e.g control, diag1, diag2) in order to compare cortical thickness in these diagnostic groups. I am coming across two main errors; 1. The first one I get upon clicking analyze in the qdec GUI I get the error: Error in Analyze: Couldn't open /subject_directory/subject/surf/lh.thickness.fwhm10.fsaverage.mgz or .mgh file. This makes sense since the subject in question did not have that file in that path. Having googled the issue, one answer pointed out that I may have needed to run recon-all -s subjid -qcache However, when I run this, nothing happens and the lh.thickness.fwhm10.fsaverage.mgz file was not created. 2. Secondly, I read on an old version of the wiki that qdec does not support more than two levels in a factor. Is this still the case? If this is not possible, can you suggest a freesurfer processing stream that might suit this type of analysis? Thank you! Gabriella ___ 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] make average explanation
Hello, I am currently trying to visualize group differences in cortical thickness across subject groups. In addition to using the qdec GUI, I am playing with the make_average_surface command as well as the make_average_subject command to then visualize in freeview or tksurfer - though I'm quite sure what the differences between make_average_surface and make_average_subject are. Can someone point to any documentation expanding on exactly what these commands do (differently)? Thank you. Gabriella ___ 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] freeview errors
Hello, I sent in a message yesterday but to no avail. I thought I would add a little more info about the error message I'm receiving. I am trying to view surfaces in 3D using Freeview on my own subject data via this script from the Freesurfer website (replacing the subject name); freeview -f good_output/surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \ good_output/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 \ good_output/surf/lh.inflated:visible=0 \ good_output/surf/lh.white:visible=0 \ good_output/surf/lh.pial While Freeview loads correctly, I get an error message in the terminal AND the GUI upon loading: MRISread(/surf/lh.pial): could not open file MRISread(/media/seagate_external/subject/surf/lh.inflated): could not open file MRISread(/media/seagate_external/subject/surf/lh.inflated): could not open file MRISread(/media/seagate_external/subject/surf/lh.white): could not open file MRISread(/media/seagate_external/subject/surf/lh.pial): could not open file I've checked all the files and each one exists in the correct path. I've tried loading the subject data from both a drobo and from an external hardrive with no luck - same errors. I've also gone through the website/google but I can't seem to find a fix for this. Any ideas on what's going on? Apologies for the repeat. Thanks! Gabriella ___ 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.
