Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

aseg2feat and aparc2feat
by Michelle Umali 29 Sep '11

29 Sep '11

Dear Freesurfers, I wanted to generate binary masks for areas found in the Freesurfer Color Lookup Table. For example, I wanted to use number 433, the Visual_V3d_l. I tried to use aseg2feat -feat featdir --aseg aparc+aseg fslmaths -featdir/reg/freesurfer/aparc+aseg.nii.gz -thr 433v uthr 433 \ featdir/reg/freesurfer/Visual_V3d_l.nii.gz The resulting image was empty. I was able to use aseg2feat for all subcortical regions, so then i used aparc2feat. However, this uses a different color table which is missing many of the regions present in the Freesurfer Color Lookup table that I would like to use. How can I get area 433 (Visual_V3d_l) from the Freesurfer Color Lookup Table so I can later run fslmaths to generate a mask? Thanks. Michelle

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Re: [Freesurfer] Mcsrch error during recon-all
by Nick Schmansky 28 Sep '11

28 Sep '11

the log does not indicate that mri_em_register exited with an error. it appears that it produced its output correctly and continued through to nearly the end of the stream. the IFLAG messages can be ignored. the log indicates that mri_label2label is exiting with an error when trying to load the label from the fsaverage directory. the fsaverage subject is symlinked to the users SUBJECTS_DIR (to save space), but sometimes this seems to cause problems on some systems. i would try copying it to your subjects dir: cd $SUBJECTS_DIR rm fsaverage cp -r $FREESURFER_HOME/subjects/fsaverage . then you just need to run the last two stages of recon-all: recon-all -s <subjid> -balabels -label-exvivo-ec or if you dont care about the Brodmann or exvivo EC labels, you dont need to run anything. for reference: https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable n. On Wed, 2011-09-28 at 17:36 -0400, Warren Winter wrote: > Hi Nick, > > > Thanks for your help. > > > The first set of errors (of the kind I described) follows the command > " mri_em_register -skull > nu.mgz /chb/freesurfer/x86_64-Linux/packages/freesurfer/dev/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta " > > > The next follows the command " mri_em_register -uns 3 -mask > brainmask.mgz > nu.mgz /chb/freesurfer/x86_64-Linux/packages/freesurfer/dev/average/RB_all_2008-03-26.gca transforms/talairach.lta" > > > The next follows the command " mri_em_register -skull -t > transforms/talairach.lta > nu_noneck.mgz /chb/freesurfer/x86_64-Linux/packages/freesurfer/dev/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta " > > > I've attached the log if you could use it for reference. > > > Best, > > > Warren > > > > > > On Sep 28, 2011, at 4:18 PM, Nick Schmansky wrote: > > > the IFLAG messages can be ignored if mri_em_register is not exiting > > with > > error. which command is running that is exiting with error? can > > you > > send that command line from the recon-all.log file? > > > > n. > > > > On Wed, 2011-09-28 at 16:02 -0400, Warren Winter wrote: > > > 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 > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)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. > > > > > > > -- > 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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Inclusion of lateral ventricle in pial surface
by Vy Dinh 28 Sep '11

28 Sep '11

Dear Experts, I noticed that the inferior horn of the lateral ventricles are not included within the pial surface while the posterior lateral ventricles are and wonder how one should go about when making corrections for the pial surface. This was observed in the subjects that I have worked with and also with the Freesurfer tutorial sample data. For the sample data, it appears that the hippocampus provides a clear delineation of the inferior and posterior lateral ventricles in the sagittal view (see attached image "bert") which was not observed with our subjects (see attached images "sub"). The segmentation of the lateral ventricles, however, looks correct (by using the segmentation label function), so I am unsure if this discrepancy affects the measurements at all. However, it is worth confirming. I look forward to reading your responses. Thank you very much, Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh(a)rush.edu<mailto:Vy_dinh@rush.edu>

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trac-all results
by Ping-Hong Yeh 28 Sep '11

28 Sep '11

Hello, The segmented left CST tracts of one of our 3T data was not satisfactory, which has only few voxels with 1000 gray values (see attached snapshot pictures for "trac-all" and "cst_prob"). The manually tracking using deterministic tractography seems OK (see cst_stremline). Any suggestions on which step may go wrong in trac-all? Thank you, Ping

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fieldsign-sess: ERROR Surf/src mismatch
by Michelle Umali 28 Sep '11

28 Sep '11

Hey Doug and Freesurfers, At the bottom is the output showing what steps didn't run. 1) Do you think I did the whole recon-all pipeline wrong? Here's what i did after I originally ran recon-all -all -label_v1: I made edits with talairach registration edits with tkregister2 and ran recon-all -all -label_v1. After that,with tkmedit I made edits to brainmask.mgz and wm-mgz, then recon-all -autorecon2-wm and autorecon 3, -label_v1. 2) Was adding the -label_v1 flag what caused the below steps to not happen and cause the mismatch? Does adding the -label_v1 flag cause recon-all to not run on the rest of the brain? If so, do I just run recon-all -autorecon2 and -autorecon3 without the -label_v1 flag? Thanks. Michelle FreeSurfer:/media/sf_windows/ subjects> recon-all -s ld07 -make all -dontrun INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 Subject 'ld07': make -n all recon-all -s /media/sf_windows/subjects/ld07 -gcareg recon-all -s /media/sf_windows/subjects/ld07 -canorm recon-all -s /media/sf_windows/subjects/ld07 -careg -careginv recon-all -s /media/sf_windows/subjects/ld07 -rmneck recon-all -s /media/sf_windows/subjects/ld07 -skull-lta recon-all -s /media/sf_windows/subjects/ld07 -calabel recon-all -s /media/sf_windows/subjects/ld07 -normalization2 recon-all -s /media/sf_windows/subjects/ld07 -maskbfs recon-all -s /media/sf_windows/subjects/ld07 -segmentation recon-all -s /media/sf_windows/subjects/ld07 -fill recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -tessellate recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -tessellate recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -smooth1 recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -smooth1 recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -inflate1 recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -inflate1 recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -qsphere recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -qsphere recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -fix recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -fix recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -white recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -white recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -white recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -white recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -white recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -white recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -smooth2 recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -smooth2 recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -inflate2 recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -inflate2 recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -inflate2 recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -inflate2 recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -sphere recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -sphere recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -surfreg recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -surfreg recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -jacobian_white recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -jacobian_white recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -avgcurv recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -avgcurv recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -cortparc recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -cortparc recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -pial recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -pial recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -pial recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -pial recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -parcstats recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -parcstats recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -cortparc2 recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -cortparc2 recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -parcstats2 recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -parcstats2 recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -cortribbon recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -cortribbon recon-all -s /media/sf_windows/subjects/ld07 -segstats recon-all -s /media/sf_windows/subjects/ld07 -aparc2aseg recon-all -s /media/sf_windows/subjects/ld07 -wmparc - Hide quoted text - On Wed, Sep 28, 2011 at 11:21 AM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu> wrote: > Hi Michelle, this almost surely means that the surfaces are out-of-synch. > You can try > recon-all -s subject -make all -dontrun > on one of your subjects. > > If everything is in synch, then it should print > make: Nothing to be done for `all'. > > If not, it should print out the steps that it would have run (if not for the > -dontrun option). > > doug > > Michelle Umali wrote: >> >> Hi Doug, >> I get the same MRISripZeros() and MRIScopyMRI Surf/src mismatch error >> when I use -sphere and not -occip in fieldsign-sess. >> >> What else should I try? >> >> Thank you. >> Michelle >> >> >> On Tue, Sep 27, 2011 at 8:51 PM, Douglas N Greve >> <greve(a)nmr.mgh.harvard.edu> wrote: >> >>> >>> Is the occip patch out of synch with the subject? Does it run if you use >>> -sphere instead of -occip? >>> doug >>> >>> Michelle Umali wrote: >>> >>>> >>>> Dear Freesurfers, >>>> This is related to my retinotopy analysis tksurfer-sess dimension >>>> mismatch error message. >>>> >>>> So another subject had these errors come up during fieldsign-sess >>>> selxavg3-sess -a rtopy.self.lh -s sjXX -force >>>> (which ran without error) >>>> >>>> then I ran fieldsign >>>> fieldsign-sess -a rtopy.self.lh -occip -s sjXX >>>> >>>> and got: >>>> ERROR: MRISripZeros(): dimension mismatch >>>> ERROR: MRIScopyMRI: Surf/Src dimension mismatch. >>>> ERROR: MRIScopyMRI: Surf/Src dimension mismatch. >>>> ERROR: MRIScopyMRI: Surf/Src dimension mismatch. >>>> ERROR: MRIScopyMRI: Surf/Src dimension mismatch. >>>> >>>> What may have caused this? >>>> >>>> Thanks. >>>> Michelle >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)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 >>> >>> >>> >>> 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(a)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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Inclusion of lateral ventricles within pial surface
by Vy Dinh 28 Sep '11

28 Sep '11

Dear Experts, Sorry for reposting this question, but I forgot to attach the images in the first post. Here is my inquiry: I noticed that the inferior horn of the lateral ventricles are not included within the pial surface while the posterior lateral ventricles are and wonder how one should go about when making corrections for the pial surface. This was observed in the subjects that I have worked with and also with the Freesurfer tutorial sample data. For the sample data, it appears that the hippocampus provides a clear delineation of the inferior and posterior lateral ventricles in the sagittal view (see attached image "bert") which was not observed with our subjects (see attached images "sub"). The segmentation of the lateral ventricles, however, looks correct (by using the segmentation label function), so I am unsure if this discrepancy affects the measurements at all. However, it is worth confirming. I look forward to reading your responses. Thank you very much, Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh(a)rush.edu<mailto:Vy_dinh@rush.edu>

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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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