[Freesurfer] Re global lgi values
Dear list, I have a question about extracting global lgi values/hemisphere. I think I have managed to do it correctly using : mri_segstats --slabel subj lh $SUBJECTS_DIR/subj/label/lh.cortex --i $SUBJECTS_DIR/subj/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats (Please let me know if this is not correct) I then get this output ( for each individual) ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 0 7953 5220.0 Seg 2.4055 0.4052 1.5796 2.9763 1.3967 2 1156737 101379.9 Seg0001 2.9472 0.9038 1.7030 6.0007 4.2977 I assume one of these values (if above command has worked correctly) contains the mean lgi value for the left hemisphere. Can somebody please tell me which of the above values is the correct lgi value? Additionally, what units are lgi measured in, and are values between 1-5 what is considered normal? Thank you very much Anna ___ 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] Re global lgi values
Thank you very much. By second I assume you mean second row? And out of the values on the second row it must be the value 2.9472? Is it headed by Area_mm2 or Mean? And what are the units? Thanks again On Wed, Nov 13, 2013 at 4:56 PM, Douglas N Greve wrote: > > that looks correct. It is the 2nd number you want. The first is for the > medial wall (not interesting). You can have it report only for cortex by > adding --id 1 > > doug > > > On 11/13/2013 11:45 AM, Anna Jonsson wrote: > > Dear list, > > > > I have a question about extracting global lgi values/hemisphere. I > > think I have managed to do it correctly using : > > > > mri_segstats --slabel subj lh $SUBJECTS_DIR/subj/label/lh.cortex --i > $SUBJECTS_DIR/subj/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats > > > > (Please let me know if this is not correct) > > > > > > I then get this output ( for each individual) > > > > ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min > Max Range > >1 0 7953 5220.0 Seg 2.4055 0.4052 1.5796 > 2.9763 1.3967 > > > >2 1156737 101379.9 Seg0001 2.9472 0.9038 1.7030 > 6.0007 4.2977 > > > > I assume one of these values (if above command has worked correctly) > contains the mean lgi value for the left hemisphere. Can somebody please > tell me which of the above values is the correct lgi value? Additionally, > what units are lgi measured in, and are values between 1-5 what is > considered normal? > > > > > > Thank you very much > > > > Anna > > > > > > ___ > > 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 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] Re global lgi values
Thank you. Can I then use aparcstats2table --subjects --hemi lh --meas thickness --parc lh.aparc.pial_lgi.stats --tablefile aparc_lgi_lh.txt to get all the values in 1 tablefile or should I use other command? On Wed, Nov 13, 2013 at 6:59 PM, Douglas N Greve wrote: > yes and yes > > > On 11/13/2013 12:04 PM, Anna Jonsson wrote: > >> Thank you very much. By second I assume you mean second row? And out of >> the values on the second row it must be the value 2.9472? Is it headed by >> Area_mm2 or Mean? And what are the units? >> >> Thanks again >> >> >> >> On Wed, Nov 13, 2013 at 4:56 PM, Douglas N Greve < >> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> >> >> that looks correct. It is the 2nd number you want. The first is >> for the >> medial wall (not interesting). You can have it report only for >> cortex by >> adding --id 1 >> >> doug >> >> >> On 11/13/2013 11:45 AM, Anna Jonsson wrote: >> > Dear list, >> > >> > I have a question about extracting global lgi values/hemisphere. I >> > think I have managed to do it correctly using : >> > >> > mri_segstats --slabel subj lh >> $SUBJECTS_DIR/subj/label/lh.cortex --i >> $SUBJECTS_DIR/subj/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats >> > >> > (Please let me know if this is not correct) >> > >> > >> > I then get this output ( for each individual) >> > >> > ColHeaders Index SegId NVertices Area_mm2 StructName Mean >> StdDev Min Max Range >> >1 0 7953 5220.0 Seg 2.4055 0.4052 >> 1.5796 2.9763 1.3967 >> > >> >2 1156737 101379.9 Seg0001 2.9472 0.9038 >> 1.7030 6.0007 4.2977 >> > >> > I assume one of these values (if above command has worked >> correctly) contains the mean lgi value for the left hemisphere. >> Can somebody please tell me which of the above values is the >> correct lgi value? Additionally, what units are lgi measured in, >> and are values between 1-5 what is considered normal? >> > >> > >> > Thank you very much >> > >> > Anna >> > >> > >> > ___ >> > Freesurfer mailing list >> > 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 >> gr...@nmr.mgh.harvard.edu <mailto:gr...@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: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://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 <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 > 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] Re Freesurfer type
Dear list members, I was wondering where in the Freesurfer output the information on which freesurfer version has been used to process scans is located? eg recon-all.log? Thank you, Kind Wishes, Anna ___ 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] Re global lgi values
Thank you. I have tried to write a script to make this above process automatic but it doesn't work. Any tips on how to make the above process into a script for a number of subjects ? Kind Wishes, Anna On Thu, Nov 14, 2013 at 7:39 PM, Douglas N Greve wrote: > I think it would be > > --parc aparc.pial_lgi > > doug > > > > On 11/14/2013 11:27 AM, Anna Jonsson wrote: > >> Thank you. Can I then use >> aparcstats2table --subjects --hemi lh --meas thickness --parc >> lh.aparc.pial_lgi.stats --tablefile aparc_lgi_lh.txt to get all the values >> in 1 tablefile or should I use other command? >> >> >> On Wed, Nov 13, 2013 at 6:59 PM, Douglas N Greve < >> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> >> yes and yes >> >> >> On 11/13/2013 12:04 PM, Anna Jonsson wrote: >> >> Thank you very much. By second I assume you mean second row? >> And out of the values on the second row it must be the value >> 2.9472? Is it headed by Area_mm2 or Mean? And what are the units? >> >> Thanks again >> >> >> >> On Wed, Nov 13, 2013 at 4:56 PM, Douglas N Greve >> mailto:gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.edu >> >> <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: >> >> >> that looks correct. It is the 2nd number you want. The >> first is >> for the >> medial wall (not interesting). You can have it report only for >> cortex by >> adding --id 1 >> >> doug >> >> >> On 11/13/2013 11:45 AM, Anna Jonsson wrote: >> > Dear list, >> > >> > I have a question about extracting global lgi >> values/hemisphere. I >> > think I have managed to do it correctly using : >> > >> > mri_segstats --slabel subj lh >> $SUBJECTS_DIR/subj/label/lh.cortex --i >> $SUBJECTS_DIR/subj/surf/lh.pial_lgi --sum >> lh.aparc.pial_lgi.stats >> > >> > (Please let me know if this is not correct) >> > >> > >> > I then get this output ( for each individual) >> > >> > ColHeaders Index SegId NVertices Area_mm2 StructName Mean >> StdDev Min Max Range >> >1 0 7953 5220.0 Seg 2.4055 0.4052 >> 1.5796 2.9763 1.3967 >> >> > >> >2 1156737 101379.9 Seg0001 2.9472 0.9038 >> 1.7030 6.0007 4.2977 >> > >> > I assume one of these values (if above command has worked >> correctly) contains the mean lgi value for the left >> hemisphere. >> Can somebody please tell me which of the above values is the >> correct lgi value? Additionally, what units are lgi >> measured in, >> and are values between 1-5 what is considered normal? >> > >> > >> > Thank you very much >> > >> > Anna >> > >> > >> > ___ >> > Freesurfer mailing list >> > 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 >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.edu >> >> <mailto:gr...@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> >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>
[Freesurfer] longitudinal process
Dear Freesurfer experts, I want to know if possible when doing longitudinal stream to put subjects with only one time-point through the processing (eg base and long runs) in order to subsequently use with the Matlab lme tools? Or better is to leave them out and only do those with 2+ times? Thank you Kind Regards, Anna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] longitudinal process
Hi thank you for reply. May I ask other question; after editing the base it says to reocnstruct with recon-all -base -tp1 -tp2 etc. Does this require that all scans are located in the same directory? (Before i used symbolic links as scans are in different directories) but i am unsure whether after editing the abse anything further is actually done to the cross runs? Thank you for your help, Anna On Tue, Feb 18, 2014 at 7:58 PM, Martin Reuter wrote: > Hi Anna, > > the linear mixed effects models can include subjects with a single time > point and it would be a shame to drop that information. That is why we > modified the longitudinal pipeline (use 5.3) to allow processing of > subjects with a single time point. However, it is necessary that these > images undergo the same processing steps as the rest of the data (to avoid > bias). So you run it exactly as other subjects, with a cross sectional, > -base and a -long step: > > recon-all -all -s -i path_to_tp1_dcm > > recon-all -base -tp -all > > recon-all -long -all > > > Best, Martin > > > On 02/18/2014 04:58 AM, Anna Jonsson wrote: > > Dear Freesurfer experts, > > I want to know if possible when doing longitudinal stream to put subjects > with only one time-point through the processing (eg base and long runs) in > order to subsequently use with the Matlab lme tools? Or better is to leave > them out and only do those with 2+ times? > > Thank you > > Kind Regards, > > Anna > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > Martin Reuter, Ph.D. > Assistant in Neuroscience - Massachusetts General Hospital > Instructor in Neurology - Harvard Medical School > MGH / HMS / MIT > > A.A.Martinos Center for Biomedical Imaging > 149 Thirteenth Street, Suite 2301 > Charlestown, MA 02129 > > Phone: +1-617-724-5652 > Email: >mreu...@nmr.mgh.harvard.edu >reu...@mit.edu > Web : http://reuter.mit.edu > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only 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] lgi for longitudinal scans
Dear group, If I want conduct gyrification analyses on the long runs that have been through the longitudinal stream, do I just perform the "normal" baseline command on the .long data? thank you, kind wishes Anna ___ 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] lgi for longitudinal scans
thank you. But if the lnog process has already been done and these induviduals already have long directories so to speak, I would just put the lgi flag on as normal but just replace the subject name with the long subject name eg ? recon-all -s _long -localGI Thank you On Sat, Mar 15, 2014 at 2:07 PM, Martin Reuter wrote: > Hi Anna, > > for the image processing, you just add the lgi flag to the regular > longitudinal recon-all command > recon-all -long .. -lgi > > for the analysis after that you use the long directories. > > Best, Martin > > On Mar 15, 2014, at 10:04 AM, Anna Jonsson wrote: > > Dear group, > > If I want conduct gyrification analyses on the long runs that have been > through the longitudinal stream, do I just perform the "normal" baseline > command on the .long data? > > thank you, > > kind wishes > > Anna > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > - > Dr. Martin Reuter > Assistant in Neuroscience - Massachusetts General Hospital > Instructor in Neurology - Harvard Medical School > MGH / HMS / MIT > > A.A.Martinos Center for Biomedical Imaging > 149 Thirteenth Street, Suite 2301 > Charlestown, MA 02129 > > Phone: +1-617-724-5652 > Email: >mreu...@nmr.mgh.harvard.edu >reu...@mit.edu > Web : http://reuter.mit.edu > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only 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] re finding sulcal folding values
Hi I would like get a mean sulcal folding value per hemisphere and roi data. I have two questions: Is possible do sulcal depth analysis using qdec? And What is the exact command to pass to mris_anatomical_stats to get a mean sulcal depth value /per hemisphere? I have tried some few variations with no luck. Thank you for your help, Kind Wishes, Anna ___ 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] re finding sulcal folding values
hi i think what i meant to write was how to find exact values for sulcal depth? using mris_anatomical_stats, so the exact command that would do this? On Wed, Apr 30, 2014 at 1:32 PM, Bruce Fischl wrote: > Hi Anna > > at the moment we take the mean out of the sulc before writing it, and use > that as kind of the definition of the transition from gyral to sulcal. We > can add a switch to mris_inflate to inhibit this behavior if you want I > suppose. > > cheers > Bruce > On Wed, 30 Apr 2014, Anna Jonsson wrote: > > > Hi I would like get a mean sulcal folding value per hemisphere and roi > data. > > I have two questions: > > > > Is possible do sulcal depth analysis using qdec? > > > > And > > > > What is the exact command to pass to mris_anatomical_stats to get a mean > > sulcal depth value /per hemisphere? I have tried some few variations > with no > > luck. > > > > Thank you for your help, > > > > Kind Wishes, > > > > Anna > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only 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 question
Dear group, when using the qdec gui interface, I was wondering where the "button" or the likes is to change the estimation from its standard doss to dods (different osnet, different slope). I believe I can do this somewhere on the qdec gui without changing to mri_glmfit? ___ 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 question
thank you. I have another question; I am getting several significant clusters for group, when correcting for multiple comparisons and total brain size and age, but when I enter sex in, msot of these disappear, but i do not understand whether this is a power issue (as qdec automatically incorporates the interaction effect) or whether this is actually a gender effect? Because the group*gender interaction is non-significant, and the main effect of gender does not have a significant effect of any of the cortical measures either? Please, any help would be greatly appreciated. Kind Wishes, Anna On Mon, May 5, 2014 at 8:39 PM, Douglas N Greve wrote: > > DOSS is not working in QDEC. It should be disabled in 5.3 > doug > > On 05/05/2014 09:39 AM, Anna Jonsson wrote: > > Dear group, > > > > when using the qdec gui interface, I was wondering where the "button" > > or the likes is to change the estimation from its standard doss to > > dods (different osnet, different slope). I believe I can do this > > somewhere on the qdec gui without changing to mri_glmfit? > > > > > > ___ > > 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 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] free-surfer longitudinal Qdec table
Hi, I would like to make my freesurfer longitudinal qdec table for the to use in the lme matlab tools. However, does the fsid need to refer to the longitidunally derived subject; eg XXX.long, or the cross-sectionally derived subject, eg XXX. Im not sure based on the specification online. Kind Regards Anna ___ 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] free-surfer longitudinal Qdec table
Hi, sorry for more questions, but i have a few. When running the first step of the lme implemented tools, doing the command *mris_preproc* --qdec-long qdec.table.dat --target study_average --hemi lh --meas thickness --out lh.thickness.mgh (assembles your thickness data into a single lh.thickness.mgh file), am I correct that this just needs to be a "normal" cross-sectional qdec table that free surfer subsequently makes into long format by --qdec-long option? so the lnogitudinal qdec table is only used in the two stage modell? This too just uses the cross-sectionally derived scans? Im confused where the .long runs become used? thank you and kind wishes On Wed, Jun 4, 2014 at 5:01 PM, Martin Reuter wrote: > Hi Anna, > Fsid is the cross sectionall name without the .long. > Best martin > > > Sent via my smartphone, please excuse brevity. > > > ---- Original message > From: Anna Jonsson > Date:06/04/2014 7:22 AM (GMT-05:00) > To: Freesurfer support list > Subject: [Freesurfer] free-surfer longitudinal Qdec table > > Hi, > > I would like to make my freesurfer longitudinal qdec table for the to use > in the lme matlab tools. However, does the fsid need to refer to the > longitidunally derived subject; eg XXX.long, or the cross-sectionally > derived subject, eg XXX. Im not sure based on the specification online. > Kind Regards > > Anna > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only 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] free-surfer longitudinal Qdec table
thank you. and one other question; rather than putting years as the time variable, can i do time 1 (for baseline) and 2 (for follow-up), and jsut control for time between scans instead? On Fri, Jun 13, 2014 at 5:42 PM, Martin Reuter wrote: > Hi Anna, whenever it says qdec-long the table is in qdec format (with a > fsid-base as second column. It would then use the longitudinally processed > results, which is what you want , both for lme and 2 stage model. > Best Martin > > > Sent via my smartphone, please excuse brevity. > > Original message ---- > From: Anna Jonsson > Date:06/09/2014 3:47 PM (GMT+01:00) > To: Freesurfer support list > Subject: Re: [Freesurfer] free-surfer longitudinal Qdec table > > Hi, sorry for more questions, but i have a few. When running the first > step of the lme implemented tools, doing the command *mris_preproc* > --qdec-long qdec.table.dat --target study_average --hemi lh --meas > thickness --out lh.thickness.mgh (assembles your thickness data into a > single lh.thickness.mgh file), am I correct that this just needs to be a > "normal" cross-sectional qdec table that free surfer subsequently makes > into long format by --qdec-long option? so the lnogitudinal qdec table is > only used in the two stage modell? This too just uses the cross-sectionally > derived scans? Im confused where the .long runs become used? > > thank you and kind wishes > > > On Wed, Jun 4, 2014 at 5:01 PM, Martin Reuter > wrote: > >> Hi Anna, >> Fsid is the cross sectionall name without the .long. >> Best martin >> >> >> Sent via my smartphone, please excuse brevity. >> >> >> Original message >> From: Anna Jonsson >> Date:06/04/2014 7:22 AM (GMT-05:00) >> To: Freesurfer support list >> Subject: [Freesurfer] free-surfer longitudinal Qdec table >> >> Hi, >> >> I would like to make my freesurfer longitudinal qdec table for the to use >> in the lme matlab tools. However, does the fsid need to refer to the >> longitidunally derived subject; eg XXX.long, or the cross-sectionally >> derived subject, eg XXX. Im not sure based on the specification online. >> Kind Regards >> >> Anna >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only 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] free-surfer longitudinal Qdec table
Thank you. I just another question about the fsid groupings for the qdec table for lme. If in the qdec I specify only the fisid (eg nt the longitudinally processed subject with XX.long), and the XX.longs are in a different folder, than how when I do the matlab lme tools does freesurfer know to use the XXX.long scans? This is confusing me. Thanks for help,. Regards Anna On Tue, Jun 24, 2014 at 11:26 AM, Martin Reuter wrote: > Hi Anna > I am not a statistician, but I would not control for duration separately, > but rather use the time variable for that. > It does not need to be in years (can be days out months). > Measures closer in time are more correlated than measures further apart. > Lme makes use of that information through the time variable. > Best Martin > Best Martin > > Sent via my smartphone, please excuse brevity. > > ---- Original message > From: Anna Jonsson > Date:06/24/2014 11:52 AM (GMT+01:00) > To: Martin Reuter > Cc: Freesurfer support list > Subject: Re: [Freesurfer] free-surfer longitudinal Qdec table > > thank you. and one other question; rather than putting years as the time > variable, can i do time 1 (for baseline) and 2 (for follow-up), and jsut > control for time between scans instead? > > > On Fri, Jun 13, 2014 at 5:42 PM, Martin Reuter < > mreu...@nmr.mgh.harvard.edu> wrote: > >> Hi Anna, whenever it says qdec-long the table is in qdec format (with a >> fsid-base as second column. It would then use the longitudinally processed >> results, which is what you want , both for lme and 2 stage model. >> Best Martin >> >> >> Sent via my smartphone, please excuse brevity. >> >> Original message >> From: Anna Jonsson >> Date:06/09/2014 3:47 PM (GMT+01:00) >> To: Freesurfer support list >> Subject: Re: [Freesurfer] free-surfer longitudinal Qdec table >> >> Hi, sorry for more questions, but i have a few. When running the first >> step of the lme implemented tools, doing the command *mris_preproc* >> --qdec-long qdec.table.dat --target study_average --hemi lh --meas >> thickness --out lh.thickness.mgh (assembles your thickness data into a >> single lh.thickness.mgh file), am I correct that this just needs to be a >> "normal" cross-sectional qdec table that free surfer subsequently makes >> into long format by --qdec-long option? so the lnogitudinal qdec table is >> only used in the two stage modell? This too just uses the cross-sectionally >> derived scans? Im confused where the .long runs become used? >> >> thank you and kind wishes >> >> >> On Wed, Jun 4, 2014 at 5:01 PM, Martin Reuter < >> mreu...@nmr.mgh.harvard.edu> wrote: >> >>> Hi Anna, >>> Fsid is the cross sectionall name without the .long. >>> Best martin >>> >>> >>> Sent via my smartphone, please excuse brevity. >>> >>> >>> Original message >>> From: Anna Jonsson >>> Date:06/04/2014 7:22 AM (GMT-05:00) >>> To: Freesurfer support list >>> Subject: [Freesurfer] free-surfer longitudinal Qdec table >>> >>> Hi, >>> >>> I would like to make my freesurfer longitudinal qdec table for the to >>> use in the lme matlab tools. However, does the fsid need to refer to the >>> longitidunally derived subject; eg XXX.long, or the cross-sectionally >>> derived subject, eg XXX. Im not sure based on the specification online. >>> Kind Regards >>> >>> Anna >>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> The information in this e-mail is intended only for the person to whom >>> it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you >>> in error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> >> > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail
Re: [Freesurfer] free-surfer longitudinal Qdec table
Ok, so even though in the qdec table you only specify the cross names as your fsid's, when you actually do the analysis the longs need to be in the same directory as the cross and bases (ie everything in the same directory) and matlab automatically uses the .long files, even though only the cross and fsid's are specified in the qdec table? Is this correct? Kind regards, Anna On Tue, Jun 24, 2014 at 7:11 PM, Martin Reuter wrote: > Hi Anna, > > the matlab tools don't know. They only look at the other co-variates that > you might want to include into your study (the fsid-base for grouping, the > time variable and others from the table). The stack of thickness maps needs > to be in the same order as the rows in the qdec table. That is why it is a > good idea to use the same table to assemble the stack (and for that you'd > use the -long-qdec flag and it uses the .long.base file names). > > Best, Martin > > > On Jun 24, 2014, at 5:23 PM, Anna Jonsson wrote: > > Thank you. I just another question about the fsid groupings for the qdec > table for lme. If in the qdec I specify only the fisid (eg nt the > longitudinally processed subject with XX.long), and the XX.longs are in a > different folder, than how when I do the matlab lme tools does freesurfer > know to use the XXX.long scans? This is confusing me. > > Thanks for help,. > > Regards Anna > > > On Tue, Jun 24, 2014 at 11:26 AM, Martin Reuter < > mreu...@nmr.mgh.harvard.edu> wrote: > >> Hi Anna >> I am not a statistician, but I would not control for duration separately, >> but rather use the time variable for that. >> It does not need to be in years (can be days out months). >> Measures closer in time are more correlated than measures further apart. >> Lme makes use of that information through the time variable. >> Best Martin >> Best Martin >> >> Sent via my smartphone, please excuse brevity. >> >> Original message >> From: Anna Jonsson >> Date:06/24/2014 11:52 AM (GMT+01:00) >> To: Martin Reuter >> Cc: Freesurfer support list >> Subject: Re: [Freesurfer] free-surfer longitudinal Qdec table >> >> thank you. and one other question; rather than putting years as the time >> variable, can i do time 1 (for baseline) and 2 (for follow-up), and jsut >> control for time between scans instead? >> >> >> On Fri, Jun 13, 2014 at 5:42 PM, Martin Reuter < >> mreu...@nmr.mgh.harvard.edu> wrote: >> >>> Hi Anna, whenever it says qdec-long the table is in qdec format (with a >>> fsid-base as second column. It would then use the longitudinally processed >>> results, which is what you want , both for lme and 2 stage model. >>> Best Martin >>> >>> >>> Sent via my smartphone, please excuse brevity. >>> >>> Original message >>> From: Anna Jonsson >>> Date:06/09/2014 3:47 PM (GMT+01:00) >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] free-surfer longitudinal Qdec table >>> >>> Hi, sorry for more questions, but i have a few. When running the first >>> step of the lme implemented tools, doing the command *mris_preproc* >>> --qdec-long qdec.table.dat --target study_average --hemi lh --meas >>> thickness --out lh.thickness.mgh (assembles your thickness data into a >>> single lh.thickness.mgh file), am I correct that this just needs to be a >>> "normal" cross-sectional qdec table that free surfer subsequently makes >>> into long format by --qdec-long option? so the lnogitudinal qdec table is >>> only used in the two stage modell? This too just uses the cross-sectionally >>> derived scans? Im confused where the .long runs become used? >>> >>> thank you and kind wishes >>> >>> >>> On Wed, Jun 4, 2014 at 5:01 PM, Martin Reuter < >>> mreu...@nmr.mgh.harvard.edu> wrote: >>> >>>> Hi Anna, >>>> Fsid is the cross sectionall name without the .long. >>>> Best martin >>>> >>>> >>>> Sent via my smartphone, please excuse brevity. >>>> >>>> >>>> Original message >>>> From: Anna Jonsson >>>> Date:06/04/2014 7:22 AM (GMT-05:00) >>>> To: Freesurfer support list >>>> Subject: [Freesurfer] free-surfer longitudinal Qdec table >>>> >>>> Hi, >>>> >>>> I would like to make my freesurfer longitudinal qdec table for the to >>>> use in the lme matlab tools. However, does the f
Re: [Freesurfer] visualize group analysis results of qdec
I also have this problem now. did this query ever resolve? On Wed, Jun 4, 2014 at 10:55 PM, Qijing Yu wrote: > Hello FreeSufers, > > I ran several analyses in qdec, and now have problem visualize previous > analyses results...which sounds dumb... Please let me know if you have any > ideas. > > I used fsaverage. I found this page > http://freesurfer.net/fswiki/FsTutorial/Visualization using tksurfer, but > it needs to do the "make_average". And it mentioned some "pre-computed > results", I thought which would be the results of analyses via command > line. Does this apply to the results by qdec? > > I also found the following command using Freeview: > freeview -f > SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 > -viewport 3d > > But I don't know which part of the command should I change. I tried the > command as it is above anyway and the error is: Unrecognized sub-option > flag 'annot_outline' > > Many thanks! All the best, > Qijing > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only 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 error
Dear group, I now have error loading my qdec table into qdec, for this error fsid column:1 Number of factors: 8 Number of subjects: 168 ERROR: QdecSubject::GetContinuousFactor failure: could not find factor name: age_demeaned for subject XXX However those 5 of those "factors" are continious, and Im assuming the problem is that for some reason qdec thinks they are categorical, and should have a file with levels corresponding to them. How I make freesurfer know they are continuous? Kind Wishes, Linn ___ 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 error
hi, i never recieved answer for this problem...any ideas? On Tue, Jul 8, 2014 at 11:13 AM, Anna Jonsson wrote: > Dear group, I now have error loading my qdec table into qdec, for this > error > > fsid column:1 > Number of factors: 8 > Number of subjects: 168 > ERROR: QdecSubject::GetContinuousFactor failure: could not find factor > name: age_demeaned for subject XXX > > However those 5 of those "factors" are continious, and Im assuming the > problem is that for some reason qdec thinks they are categorical, and > should have a file with levels corresponding to them. How I make freesurfer > know they are continuous? > > Kind Wishes, > > Linn > > ___ 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] lgi for longitudinal scans
hi Martin, I just tried this and it resulted in errors/ Do I not have to specify a flag for the baseid or for each subject, eg -s? What I did (according to your suggestion) recon-all -long XXX_1.long XXX_2.long -localGI This did not work? Do you know why potentially? On Wed, Mar 26, 2014 at 3:28 PM, Martin Reuter wrote: > Hi Anna, > > no, you would still do: > > recon-all -long tpid baseid -localGI > > just not use the '-all'. > > Best, Martin > > > > > On 03/26/2014 11:12 AM, Anna Jonsson wrote: > > thank you. But if the lnog process has already been done and these > induviduals already have long directories so to speak, I would just put the > lgi flag on as normal but just replace the subject name with the long > subject name eg ? > > recon-all -s _long -localGI > > > Thank you > > > > On Sat, Mar 15, 2014 at 2:07 PM, Martin Reuter < > mreu...@nmr.mgh.harvard.edu> wrote: > >> Hi Anna, >> >> for the image processing, you just add the lgi flag to the regular >> longitudinal recon-all command >> recon-all -long …… -lgi >> >> for the analysis after that you use the long directories. >> >> Best, Martin >> >> On Mar 15, 2014, at 10:04 AM, Anna Jonsson >> wrote: >> >> Dear group, >> >> If I want conduct gyrification analyses on the long runs that have been >> through the longitudinal stream, do I just perform the "normal" baseline >> command on the .long data? >> >> thank you, >> >> kind wishes >> >> Anna >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> - >> Dr. Martin Reuter >> Assistant in Neuroscience - Massachusetts General Hospital >> Instructor in Neurology - Harvard Medical School >> MGH / HMS / MIT >> >> A.A.Martinos Center for Biomedical Imaging >> 149 Thirteenth Street, Suite 2301 >> Charlestown, MA 02129 >> >> Phone: +1-617-724-5652 >> Email: >>mreu...@nmr.mgh.harvard.edu >>reu...@mit.edu >> Web : http://reuter.mit.edu >> >> >> ___ >> 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. >> >> > > -- > Martin Reuter, Ph.D. > > Instructor in Neurology > Harvard Medical School > Assistant in Neuroscience > Dept. of Radiology, Massachusetts General Hospital > Dept. of Neurology, Massachusetts General Hospital > Research Affiliate > Computer Science and Artificial Intelligence Lab, > Dept. of Electrical Engineering and Computer Science, > Massachusetts Institute of Technology > > A.A.Martinos Center for Biomedical Imaging > 149 Thirteenth Street, Suite 2301 > Charlestown, MA 02129 > > Phone: +1-617-724-5652 > > Email: >mreu...@nmr.mgh.harvard.edu >reu...@mit.edu > Web : http://reuter.mit.edu > > ___ 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] prefrontal cortex label
Dear group, Is there a way to create a prefrontal cortex label in fresurfer? if so, please tell me the exact steps to do so, I am very confused. Thank you, Anna ___ 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] prefrontal cortex label
thank you. which labels are normally included as prefrontal cortex for freesurfer purposes? On Thu, Oct 23, 2014 at 5:04 PM, Douglas N Greve wrote: > > You can use mri_annotation2label to break up the annotation into > individual labels, then use mris_label2annot to recombine selected > labels into an annotation or use mri_merge_label to merge them into a > single label. All you have to do is decide with labels define prefontal > doug > > > On 10/23/2014 10:25 AM, Anna Jonsson wrote: > > Dear group, > > > > Is there a way to create a prefrontal cortex label in fresurfer? if > > so, please tell me the exact steps to do so, I am very confused. > > > > > > Thank you, > > > > Anna > > > > > > ___ > > 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 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] prefrontal cortex label
hi, anyone can help with this? On Tue, Nov 4, 2014 at 4:43 PM, Douglas N Greve wrote: > I don't know. Maybe someone else can weigh in. > doug > > On 11/04/2014 07:38 AM, Anna Jonsson wrote: > > thank you. which labels are normally included as prefrontal cortex for > > freesurfer purposes? > > > > On Thu, Oct 23, 2014 at 5:04 PM, Douglas N Greve > > mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > > > You can use mri_annotation2label to break up the annotation into > > individual labels, then use mris_label2annot to recombine selected > > labels into an annotation or use mri_merge_label to merge them into a > > single label. All you have to do is decide with labels define > > prefontal > > doug > > > > > > On 10/23/2014 10:25 AM, Anna Jonsson wrote: > > > Dear group, > > > > > > Is there a way to create a prefrontal cortex label in fresurfer? if > > > so, please tell me the exact steps to do so, I am very confused. > > > > > > > > > Thank you, > > > > > > Anna > > > > > > > > > ___ > > > Freesurfer mailing list > > > 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 > > gr...@nmr.mgh.harvard.edu <mailto:gr...@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: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://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 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 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] prefrontal cortex label
hi, I have tried to make prefrotnal cortex label by doing first mri_annotation2label --subject "$subject" --hemi rh --outdir "$subject"/label mri_mergelabels -i lh.caudalanteriorcingulate.label -i lh.caudalmiddlefrontal.label -i lh.lateralorbitofrontal.label -i lh.medialorbitofrontal.label -i lh.parsopercularis.label -i lh.parsorbitalis.label -i lh.parstriangularis.label -i lh.rostralanteriorcingulate.label -i lh.rostralmiddlefrontal.label -i lh.superiorfrontal.label -i lh.lateralorbitofrontal.label -o lh.prefrontalcortex.label -d /directory/subject/label which does create a label called x.prefrontalcortex.label in each persons directory. then however when i try to do mris_anatomical_stats -l $SUBJECTS_DIR/"$subject"/label/lh.prefrontalcortex.label "$subject" lh pial | grep "thickness" >> left_prefrontal i get error and say it cant find label. any pointers on what im doing wrong? thank you ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] prefrontal cortex label
hi the full error message is reading input surface /XX/surf/lh.pial... reading input pial surface /XX/surf/lh.pial... reading input white surface //X/surf/lh.white... mris_anatomical_stats: could not parse 1697283th line '60529 -5.365 -17' in label file subj: could not read label file (null) On Mon, Nov 24, 2014 at 4:56 PM, Douglas N Greve wrote: > What is the full terminal output and error msg? > > On 11/21/2014 04:14 AM, Anna Jonsson wrote: > > hi, I have tried to make prefrotnal cortex label by doing first > > > > > > > > mri_annotation2label --subject "$subject" --hemi rh --outdir > > "$subject"/label > > > > > > > > mri_mergelabels -i lh.caudalanteriorcingulate.label -i > > lh.caudalmiddlefrontal.label -i lh.lateralorbitofrontal.label -i > > lh.medialorbitofrontal.label -i lh.parsopercularis.label -i > > lh.parsorbitalis.label -i lh.parstriangularis.label -i > > lh.rostralanteriorcingulate.label -i lh.rostralmiddlefrontal.label -i > > lh.superiorfrontal.label -i lh.lateralorbitofrontal.label -o > > lh.prefrontalcortex.label -d /directory/subject/label > > > > > > which does create a label called x.prefrontalcortex.label in each > > persons directory. then however when i try to do > > > > mris_anatomical_stats -l > > $SUBJECTS_DIR/"$subject"/label/lh.prefrontalcortex.label "$subject" lh > > pial | grep "thickness" >> left_prefrontal > > > > i get error and say it cant find label. any pointers on what im doing > > wrong? > > > > thank you > > > > > > > > > > > > ___ > > 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 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.
