Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Mcsrch error during recon-all
by Warren Winter 28 Sep '11

28 Sep '11

Hi, Each time I have run recon-all on our subjects, I end up with the same slew of error messages underneath "Computing MAP estimate using [x number of] samples" and underneath "EM alignment process": "IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCES" At the very end of the log file I see: "Loading source label. Abort Linux rc-twice 2.6.39.2-mosix #1 SMP Wed Jun 29 11:53:08 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 5 exited with ERRORS at Tue Sep 27 03:23:46 EDT 2011" Any help on this would be greatly appreciated. Best, Warren -- Warren Winter Lab Coordinator Children's Hospital Boston Division of Developmental Medicine 1 Autumn Street, AU 650 Boston, MA 02215 857-218-5224

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Re: [Freesurfer] THANKS
by Douglas N Greve 28 Sep '11

28 Sep '11

Oh, sorry, I precompute the tables with certain fixed voxel-wise thresholds. But it seems like you may want to use 2.3. Why 1.7? If you want it to match what you see in QDEC at a threshold of 2.0, then you should spec 2.3. Antonella Kis wrote: > I am not sure but I tried that and it gives me error: > > > ? --glmdir Untitled.glmdir \ > ? --cache 1.7 neg\ > ? --overwrite > ERROR: thresh = 1.7, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 > So how should I fix that? > > Many thanks! > AK > ------------------------------------------------------------------------ > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *To:* Antonella Kis <atorok9(a)yahoo.com>; freesurfer > <freesurfer(a)nmr.mgh.harvard.edu> > *Sent:* Wednesday, September 28, 2011 4:07 PM > *Subject:* Re: [Freesurfer] THANKS > > The change in threshold is always 0.3. Eg, to go from a two-tailed > threshold of 2.0 to a one-tailed threshold, you would subtract .3 from > 2.0 (and so 1.7). Is this what you mean? > > Antonella Kis wrote: > > I see. Is there a way that I can get/read both clusters sin other > words can I eliminate this inconvenient of two-tailed p-value? > > > > Thanks, > > AK > > > > ------------------------------------------------------------------------ > > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > *To:* Antonella Kis <atorok9(a)yahoo.com <mailto:atorok9@yahoo.com>>; > freesurfer <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > *Sent:* Wednesday, September 28, 2011 2:59 PM > > *Subject:* Re: [Freesurfer] THANKS > > > > *By default, FreeSurfer compputes and uses a two-tailed p-value. When > > you specify a sign, it lowers the threshold that you give it to reflect > > a one-tailed test. Probably what happened was that you had two clusters > > close to each other that merged together with the lower threshold. > > doug > > * > > Antonella Kis wrote: > > > Dear Doug, > > > > > > Finally I've got it. But there is one more problem: when I run the > > > QDEC with Min threshold 2 neg, I am getting 2 clusters, while when I > > > am running the results from QDEC(under Untitled.glmdir) with the -sim: > > > > > > mri_glmfit-sim \ > > > --glmdir Untitled.glmdir \ > > > --cache 2 pos \ > > > --overwrite > > > > > > I am getting only one of the clusters. Can you please advise me what > > > is going on or what should I correct? > > > > > > Many thanks, > > > AK > > > > ------------------------------------------------------------------------ > > > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > > > *To:* Antonella Kis <atorok9(a)yahoo.com <mailto:atorok9@yahoo.com> > <mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com>>>; freesurfer > > > <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > *Sent:* Wednesday, September 28, 2011 1:33 PM > > > *Subject:* Re: [Freesurfer] Error with mri_glmfit-sim > > > > > > again, FDR should have nothing to do with it. If you want a voxel-wise > > > threshold at 2, just set that threshold when you run mri_glmfit-sim > > > with "--cache 2 sign" where sign is pos, neg, or abs > > > doug > > > > > > Antonella Kis wrote: > > > > Hi Doug, > > > > > > > > Thanks again for helping. I am trying to use QDEC but there are no > > > clusters surviving after FDR (it says statics cannot be done so gives > > > me error by running FDR). So I am trying to get the thickness values > > > only for the clusters that are formed in QDEC after setting up a > > > threshold = 2 (before running FDR). In order to do this you suggested > > > me to run mri_glmfit-sim on the QDEC results. The only problem is that > > > I cannot run the -sim if there is no FDR data (stats) so I cannot > > > cache the clusters formed only by thresh 2 in QDEC. Is theer a way to > > > do it? > > > > > > > > Many thanks, > > > > AK > > > > > > > > > ------------------------------------------------------------------------ > > > > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> > > > > *To:* Antonella Kis <atorok9(a)yahoo.com > <mailto:atorok9@yahoo.com> <mailto:atorok9@yahoo.com > <mailto:atorok9@yahoo.com>> <mailto:atorok9@yahoo.com > <mailto:atorok9@yahoo.com> <mailto:atorok9@yahoo.com > <mailto:atorok9@yahoo.com>>>> > > > > *Cc:* "freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>>" > > > <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>>> > > > > *Sent:* Wednesday, September 28, 2011 12:06 PM > > > > *Subject:* Re: [Freesurfer] Error with mri_glmfit-sim > > > > > > > > What does FDR have to do with it? FDR should not come into play > in this. > > > > doug > > > > > > > > Antonella Kis wrote: > > > > > Good morning Doug, > > > > > > > > > > I tried running the -sim on my QDEC output (as you recommended > me last > > > > > days) but for some data the FDR gives me error (cannot calculate > > > > > clusters statistics) so mri_glmfit-sim is not working either > since the > > > > > corrections by multiple comparisons is not working. What > should I do > > > > > in this case so I can get as output my cortical thickness > values for > > > > > the formed clusters at threshold 2, before multiple comparison? > > > > > > > > > > Many thanks, > > > > > AK > > > > > > > > -- Douglas N. Greve, Ph.D. > > > > MGH-NMR Center > > > > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> > > > > Phone Number: 617-724-2358 > > > > Fax: 617-726-7422 > > > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > The information in this e-mail is intended only for the person to > > > whom it is > > > > addressed. If you believe this e-mail was sent to you in error and > > > the e-mail > > > > contains patient information, please contact the Partners Compliance > > > HelpLine at > > > > http://www.partners.org/complianceline . If the e-mail was sent to > > > you in error > > > > but does not contain patient information, please contact the sender > > > and properly > > > > dispose of the e-mail. > > > > > > > > > > > > > > > > > > -- Douglas N. Greve, Ph.D. > > > MGH-NMR Center > > > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > > Phone Number: 617-724-2358 Fax: 617-726-7422 > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > > > > > > > > > -- Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] THANKS
by Douglas N Greve 28 Sep '11

28 Sep '11

The change in threshold is always 0.3. Eg, to go from a two-tailed threshold of 2.0 to a one-tailed threshold, you would subtract .3 from 2.0 (and so 1.7). Is this what you mean? Antonella Kis wrote: > I see. Is there a way that I can get/read both clusters sin other > words can I eliminate this inconvenient of two-tailed p-value? > > Thanks, > AK > > ------------------------------------------------------------------------ > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *To:* Antonella Kis <atorok9(a)yahoo.com>; freesurfer > <freesurfer(a)nmr.mgh.harvard.edu> > *Sent:* Wednesday, September 28, 2011 2:59 PM > *Subject:* Re: [Freesurfer] THANKS > > *By default, FreeSurfer compputes and uses a two-tailed p-value. When > you specify a sign, it lowers the threshold that you give it to reflect > a one-tailed test. Probably what happened was that you had two clusters > close to each other that merged together with the lower threshold. > doug > * > Antonella Kis wrote: > > Dear Doug, > > > > Finally I've got it. But there is one more problem: when I run the > > QDEC with Min threshold 2 neg, I am getting 2 clusters, while when I > > am running the results from QDEC(under Untitled.glmdir) with the -sim: > > > > mri_glmfit-sim \ > > --glmdir Untitled.glmdir \ > > --cache 2 pos \ > > --overwrite > > > > I am getting only one of the clusters. Can you please advise me what > > is going on or what should I correct? > > > > Many thanks, > > AK > > ------------------------------------------------------------------------ > > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > *To:* Antonella Kis <atorok9(a)yahoo.com <mailto:atorok9@yahoo.com>>; > freesurfer > > <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > *Sent:* Wednesday, September 28, 2011 1:33 PM > > *Subject:* Re: [Freesurfer] Error with mri_glmfit-sim > > > > again, FDR should have nothing to do with it. If you want a voxel-wise > > threshold at 2, just set that threshold when you run mri_glmfit-sim > > with "--cache 2 sign" where sign is pos, neg, or abs > > doug > > > > Antonella Kis wrote: > > > Hi Doug, > > > > > > Thanks again for helping. I am trying to use QDEC but there are no > > clusters surviving after FDR (it says statics cannot be done so gives > > me error by running FDR). So I am trying to get the thickness values > > only for the clusters that are formed in QDEC after setting up a > > threshold = 2 (before running FDR). In order to do this you suggested > > me to run mri_glmfit-sim on the QDEC results. The only problem is that > > I cannot run the -sim if there is no FDR data (stats) so I cannot > > cache the clusters formed only by thresh 2 in QDEC. Is theer a way to > > do it? > > > > > > Many thanks, > > > AK > > > > > > > ------------------------------------------------------------------------ > > > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > > *To:* Antonella Kis <atorok9(a)yahoo.com <mailto:atorok9@yahoo.com> > <mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com>>> > > > *Cc:* "freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>" > > <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > *Sent:* Wednesday, September 28, 2011 12:06 PM > > > *Subject:* Re: [Freesurfer] Error with mri_glmfit-sim > > > > > > What does FDR have to do with it? FDR should not come into play in > this. > > > doug > > > > > > Antonella Kis wrote: > > > > Good morning Doug, > > > > > > > > I tried running the -sim on my QDEC output (as you recommended > me last > > > > days) but for some data the FDR gives me error (cannot calculate > > > > clusters statistics) so mri_glmfit-sim is not working either > since the > > > > corrections by multiple comparisons is not working. What should I do > > > > in this case so I can get as output my cortical thickness values for > > > > the formed clusters at threshold 2, before multiple comparison? > > > > > > > > Many thanks, > > > > AK > > > > > > -- Douglas N. Greve, Ph.D. > > > MGH-NMR Center > > > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > > Phone Number: 617-724-2358 > > > Fax: 617-726-7422 > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > The information in this e-mail is intended only for the person to > > whom it is > > > addressed. If you believe this e-mail was sent to you in error and > > the e-mail > > > contains patient information, please contact the Partners Compliance > > HelpLine at > > > http://www.partners.org/complianceline . If the e-mail was sent to > > you in error > > > but does not contain patient information, please contact the sender > > and properly > > > dispose of the e-mail. > > > > > > > > > > > > > -- Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > Phone Number: 617-724-2358 Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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aseg2feat for PPI seeds for FSL
by Michelle Umali 28 Sep '11

28 Sep '11

Hi Freesurfers, I want to do a PPI in FSL FEAT using the V1 left and righ found generated in recon-all as seeds using: I know for each subject I have to get a timecourse for my seeds fslmeants -i filtered_func.nii.gz -o my_timecourse.txt -m V1_mask.nii.gz For each subject, I've run reg-feat2anat on my FEAT data from each of 4 runs. I have 2 questions: 1) Does it matter which run's FEAT I use for aseg2feat --feat featdir --aseg aparc+aseg to generate the binary masks for my seeds? 2) Does fslmeants need a special registered filtered_func.nii.gz from a cross-run GFEAT? If so, how do you specify it for this and then for actual PPI analysis in fsl? Thanks. Michelle

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Re: [Freesurfer] Error with mri_glmfit-sim
by Douglas N Greve 28 Sep '11

28 Sep '11

No, unfortunately not. doug jm wrote: > Doug: > > I have processed 20 subjects. By mistake, five of them with LAS > orientation and 15 RAS orientation.RAS that's right in my case. > I could change name of files in '/surf' folder from left to right in the > first ones? or I need do it over? for instance: I could change name of > file rh.thickness.fwhm25.fsaverage to lh.thickness.fwhm25.fsaverage? or > that have others implications to statistical analysis outcomes > > thanks > > > > On Wed, 2011-09-28 at 13:33 -0400, Douglas N Greve wrote: > >> again, FDR should have nothing to do with it. If you want a voxel-wise >> threshold at 2, just set that threshold when you run mri_glmfit-sim with >> "--cache 2 sign" where sign is pos, neg, or abs >> doug >> >> Antonella Kis wrote: >> >>> Hi Doug, >>> >>> Thanks again for helping. I am trying to use QDEC but there are no >>> clusters surviving after FDR (it says statics cannot be done so gives >>> me error by running FDR). So I am trying to get the thickness values >>> only for the clusters that are formed in QDEC after setting up a >>> threshold = 2 (before running FDR). In order to do this you suggested >>> me to run mri_glmfit-sim on the QDEC results. The only problem is that >>> I cannot run the -sim if there is no FDR data (stats) so I cannot >>> cache the clusters formed only by thresh 2 in QDEC. Is theer a way to >>> do it? >>> >>> Many thanks, >>> AK >>> >>> ------------------------------------------------------------------------ >>> *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> >>> *To:* Antonella Kis <atorok9(a)yahoo.com> >>> *Cc:* "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >>> *Sent:* Wednesday, September 28, 2011 12:06 PM >>> *Subject:* Re: [Freesurfer] Error with mri_glmfit-sim >>> >>> What does FDR have to do with it? FDR should not come into play in this. >>> doug >>> >>> Antonella Kis wrote: >>> >>>> Good morning Doug, >>>> >>>> I tried running the -sim on my QDEC output (as you recommended me last >>>> days) but for some data the FDR gives me error (cannot calculate >>>> clusters statistics) so mri_glmfit-sim is not working either since the >>>> corrections by multiple comparisons is not working. What should I do >>>> in this case so I can get as output my cortical thickness values for >>>> the formed clusters at threshold 2, before multiple comparison? >>>> >>>> Many thanks, >>>> AK >>>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)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. >>> >>> >>> >>> > > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] THANKS
by Douglas N Greve 28 Sep '11

28 Sep '11

*By default, FreeSurfer compputes and uses a two-tailed p-value. When you specify a sign, it lowers the threshold that you give it to reflect a one-tailed test. Probably what happened was that you had two clusters close to each other that merged together with the lower threshold. doug * Antonella Kis wrote: > Dear Doug, > > Finally I've got it. But there is one more problem: when I run the > QDEC with Min threshold 2 neg, I am getting 2 clusters, while when I > am running the results from QDEC(under Untitled.glmdir) with the -sim: > > mri_glmfit-sim \ > --glmdir Untitled.glmdir \ > --cache 2 pos \ > --overwrite > > I am getting only one of the clusters. Can you please advise me what > is going on or what should I correct? > > Many thanks, > AK > ------------------------------------------------------------------------ > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *To:* Antonella Kis <atorok9(a)yahoo.com>; freesurfer > <freesurfer(a)nmr.mgh.harvard.edu> > *Sent:* Wednesday, September 28, 2011 1:33 PM > *Subject:* Re: [Freesurfer] Error with mri_glmfit-sim > > again, FDR should have nothing to do with it. If you want a voxel-wise > threshold at 2, just set that threshold when you run mri_glmfit-sim > with "--cache 2 sign" where sign is pos, neg, or abs > doug > > Antonella Kis wrote: > > Hi Doug, > > > > Thanks again for helping. I am trying to use QDEC but there are no > clusters surviving after FDR (it says statics cannot be done so gives > me error by running FDR). So I am trying to get the thickness values > only for the clusters that are formed in QDEC after setting up a > threshold = 2 (before running FDR). In order to do this you suggested > me to run mri_glmfit-sim on the QDEC results. The only problem is that > I cannot run the -sim if there is no FDR data (stats) so I cannot > cache the clusters formed only by thresh 2 in QDEC. Is theer a way to > do it? > > > > Many thanks, > > AK > > > > ------------------------------------------------------------------------ > > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > *To:* Antonella Kis <atorok9(a)yahoo.com <mailto:atorok9@yahoo.com>> > > *Cc:* "freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>" > <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > *Sent:* Wednesday, September 28, 2011 12:06 PM > > *Subject:* Re: [Freesurfer] Error with mri_glmfit-sim > > > > What does FDR have to do with it? FDR should not come into play in this. > > doug > > > > Antonella Kis wrote: > > > Good morning Doug, > > > > > > I tried running the -sim on my QDEC output (as you recommended me last > > > days) but for some data the FDR gives me error (cannot calculate > > > clusters statistics) so mri_glmfit-sim is not working either since the > > > corrections by multiple comparisons is not working. What should I do > > > in this case so I can get as output my cortical thickness values for > > > the formed clusters at threshold 2, before multiple comparison? > > > > > > Many thanks, > > > AK > > > > -- Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > The information in this e-mail is intended only for the person to > whom it is > > addressed. If you believe this e-mail was sent to you in error and > the e-mail > > contains patient information, please contact the Partners Compliance > HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > > but does not contain patient information, please contact the sender > and properly > > dispose of the e-mail. > > > > > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Folding Index and Gyrification index
by Alan Francis 28 Sep '11

28 Sep '11

Hi Bruce, Nick & Doug: How does Folding index differ from Gyrification index? thanks, Alan BIDMC

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Re: [Freesurfer] Error with mri_glmfit-sim
by Douglas N Greve 28 Sep '11

28 Sep '11

again, FDR should have nothing to do with it. If you want a voxel-wise threshold at 2, just set that threshold when you run mri_glmfit-sim with "--cache 2 sign" where sign is pos, neg, or abs doug Antonella Kis wrote: > Hi Doug, > > Thanks again for helping. I am trying to use QDEC but there are no > clusters surviving after FDR (it says statics cannot be done so gives > me error by running FDR). So I am trying to get the thickness values > only for the clusters that are formed in QDEC after setting up a > threshold = 2 (before running FDR). In order to do this you suggested > me to run mri_glmfit-sim on the QDEC results. The only problem is that > I cannot run the -sim if there is no FDR data (stats) so I cannot > cache the clusters formed only by thresh 2 in QDEC. Is theer a way to > do it? > > Many thanks, > AK > > ------------------------------------------------------------------------ > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *To:* Antonella Kis <atorok9(a)yahoo.com> > *Cc:* "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > *Sent:* Wednesday, September 28, 2011 12:06 PM > *Subject:* Re: [Freesurfer] Error with mri_glmfit-sim > > What does FDR have to do with it? FDR should not come into play in this. > doug > > Antonella Kis wrote: > > Good morning Doug, > > > > I tried running the -sim on my QDEC output (as you recommended me last > > days) but for some data the FDR gives me error (cannot calculate > > clusters statistics) so mri_glmfit-sim is not working either since the > > corrections by multiple comparisons is not working. What should I do > > in this case so I can get as output my cortical thickness values for > > the formed clusters at threshold 2, before multiple comparison? > > > > Many thanks, > > AK > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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. > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Fwd: Fwd: FW: flipped orientation in tksurfer and tkmedit
by Ilana Hairston 28 Sep '11

28 Sep '11

Hi Doug, Sorry, that this is turning into a saga. The xhemireg command ran, but then recon-all failed (we used recon-all -all). Also it seems there are missing surfaces, we can't load wm and pial, the surf directory is empty. Although that maybe because the recon didn't run. Thanks i. ---------- Forwarded message ---------- From: Chelsea Cummiford <chelsea.cummiford(a)gmail.com> Date: Thu, Sep 22, 2011 at 4:35 PM Subject: Re: [Freesurfer] Fwd: FW: flipped orientation in tksurfer and tkmedit To: Ilana Hairston <hairstonster(a)gmail.com> [chelsea@hypnos ilanagroup]$ recon-all -all -subjid FlippedFS091205dc/ Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /usr/local/FS51/subjects/ilanagroup Actual FREESURFER_HOME /usr/local/FS51 -rw-rw-r-- 1 chelsea ZL 16132 Sep 22 15:37 /usr/local/FS51/subjects/ilanagroup/FlippedFS091205dc/scripts/recon-all.log Linux hypnos 2.6.18-238.el5 #1 SMP Thu Jan 13 15:51:15 EST 2011 x86_64 x86_64 x86_64 GNU/Linux #-------------------------------------------- #@# MotionCor Thu Sep 22 16:35:06 EDT 2011 ERROR: no run data found in /usr/local/FS51/subjects/ilanagroup/FlippedFS091205dc/mri. Make sure to have a volume called 001.mgz in /usr/local/FS51/subjects/ilanagroup/FlippedFS091205dc/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Linux hypnos 2.6.18-238.el5 #1 SMP Thu Jan 13 15:51:15 EST 2011 x86_64 x86_64 x86_64 GNU/Linux recon-all -s FlippedFS091205dc exited with ERRORS at Thu Sep 22 16:35:06 EDT 2011 For more details, see the log file /usr/local/FS51/subjects/ilanagroup/FlippedFS091205dc/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting On Thu, Sep 22, 2011 at 4:32 PM, Ilana Hairston <hairstonster(a)gmail.com>wrote: > can you paste in the errors? i'll forward them to the freesurfer list > > > On Thu, Sep 22, 2011 at 3:43 PM, Chelsea Cummiford < > chelsea.cummiford(a)gmail.com> wrote: > >> ok, so the xhemireg command ran fine, but I can't run recon-all -all - it >> exits with errors. says that there is no 001.mgz file. >> >> I can pull it up in tkmedit (albeit, none of the control points or >> grey/white matter lines show up). the brain is flipped compared to the >> original though. >> >> >> On Thu, Sep 22, 2011 at 3:30 PM, Chelsea Cummiford < >> chelsea.cummiford(a)gmail.com> wrote: >> >>> oh, got it. i thought you meant check both commands... will do. >>> >>> >>> On Thu, Sep 22, 2011 at 3:26 PM, Ilana Hairston <hairstonster(a)gmail.com>wrote: >>> >>>> no this one, to invert the brains that are already processed >>>> >>>> xhemireg --s reversedsubject --o newsubjectname --all-vol --noreg >>>> >>>> >>>> On Thu, Sep 22, 2011 at 3:24 PM, Chelsea Cummiford < >>>> chelsea.cummiford(a)gmail.com> wrote: >>>> >>>>> do you mean running the --in-orientation ras command and then running >>>>> recon-all?? because we did that and it looks fine in tkmedit and tksurfer - >>>>> right heng? this is what FS00wh is... >>>>> >>>>> >>>>> On Thu, Sep 22, 2011 at 2:57 PM, Ilana Hairston < >>>>> hairstonster(a)gmail.com> wrote: >>>>> >>>>>> Seems like we need to be 100% sure that our analyze/nifti is RAS. >>>>>> Chelsea, could you check the second command, followed by recon-all (i >>>>>> assume recon-all all) ? >>>>>> thx >>>>>> i >>>>>> >>>>>> >>>>>> >>>>>>> We think that in order to avoid this in future we should add a >>>>>>> --in-orientation ras flag to mri_convert. Is that correct? >>>>>>> >>>>>> >>>>>> That might work. The orientation string is actually more specific than >>>>>> just "RAS". You data might in an RAS cooridnate system, but this means that >>>>>> the orientation string could be RAS, or it could be SAR, or ARS, or ARS, >>>>>> etc. See what I mean? If it shows up correctly in tkmedit, then you're got >>>>>> it right (assuming that you are sure that it is really in an RAS coordinate >>>>>> system). >>>>>> >>>>>> >>>>>>> The other question is - now that we have processed some 50 subjects, >>>>>>> is there a way of flipping the results so that we wont have to start from >>>>>>> scratch (this is a longitudinal study and participants will be scanned >>>>>>> again).? >>>>>>> >>>>>> You can try using >>>>>> xhemireg --s reversedsubject --o newsubjectname --all-vol --noreg >>>>>> >>>>>> This script was never intended for this purpose, so I don't know >>>>>> whether it will work fully or not. It should at least reverse all the >>>>>> volumes after which you can run recon-all on it. It should keep any edits >>>>>> you have made, but the control points won't be copied (and would be wrong in >>>>>> the reversed subject). >>>>>> >>>>>> doug >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>> Thanks >>>>>>> Ilana >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> >>>>>>>> ****************************** >>>>>>>> Ilana Hairston ,PhD >>>>>>>> Research Assistant Professor >>>>>>>> 4250 Plymouth Rd. (rm 2439) >>>>>>>> Psychiatry Department, Addiction Research Center >>>>>>>> University of Michigan, Ann Arbor MI 48109-2700 >>>>>>>> Tel: 734-232-0232; Mobile: 650-906-8449 >>>>>>>> >>>>>>>> ******************** >>>>>>>> Reminder: Women do 66% of the work worldwide, earn 10% of the >>>>>>>> income, and own 1% of the world's property >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> -- >>>>>> Douglas N. Greve, Ph.D. >>>>>> MGH-NMR Center >>>>>> greve(a)nmr.mgh.harvard.edu >>>>>> Phone Number: 617-724-2358 Fax: 617-726-7422 >>>>>> >>>>>> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>>>> FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>>>> >>>>>> >>>>>> >>>>>> 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<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. >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> >>>>>> ****************************** >>>>>> Ilana Hairston ,PhD >>>>>> Research Assistant Professor >>>>>> 4250 Plymouth Rd. (rm 2439) >>>>>> Psychiatry Department, Addiction Research Center >>>>>> University of Michigan, Ann Arbor MI 48109-2700 >>>>>> Tel: 734-232-0232; Mobile: 650-906-8449 >>>>>> >>>>>> ******************** >>>>>> Reminder: Women do 66% of the work worldwide, earn 10% of the income, >>>>>> and own 1% of the world's property >>>>>> >>>>>> >>>>>> >>>>> >>>> >>>> >>>> -- >>>> >>>> ****************************** >>>> Ilana Hairston ,PhD >>>> Research Assistant Professor >>>> 4250 Plymouth Rd. (rm 2439) >>>> Psychiatry Department, Addiction Research Center >>>> University of Michigan, Ann Arbor MI 48109-2700 >>>> Tel: 734-232-0232; Mobile: 650-906-8449 >>>> >>>> ******************** >>>> Reminder: Women do 66% of the work worldwide, earn 10% of the income, >>>> and own 1% of the world's property >>>> >>>> >>>> >>> >> > > > -- > > ****************************** > Ilana Hairston ,PhD > Research Assistant Professor > 4250 Plymouth Rd. (rm 2439) > Psychiatry Department, Addiction Research Center > University of Michigan, Ann Arbor MI 48109-2700 > Tel: 734-232-0232; Mobile: 650-906-8449 > > ******************** > Reminder: Women do 66% of the work worldwide, earn 10% of the income, and > own 1% of the world's property > > > -- ****************************** Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232; Mobile: 650-906-8449 ******************** Reminder: Women do 66% of the work worldwide, earn 10% of the income, and own 1% of the world's property

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GM, WM and CSF segmentation for partial volume correction
by _andreia_＠sapo.pt 28 Sep '11

28 Sep '11

Hello list, Following this email that I found in the archives: "(...) For the segmentation, FS still works voxelwise, but it's objective is to identify each structure as a whole, whereas SPM and FSL/FAST attempt to classify each voxel as being GM, WM or CSF. A short description of the method in FS is here: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferAnalysisPipelineOverview… You may want also to have a look at this paper: http://dx.doi.org/10.1016/S0896-6273(02)00569-X Hope this helps! All the best, Anderson" I need to obtain the different % of tissue (GM, WM and CSF) inside one defined voxel. Does FS has a file that can be exported to Matlab to then get these values? Or only FSL/FAST and SPM have this type of info? Thanks! Andreia

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