[Freesurfer] volume of CSF for hemispheres
Dear list, I would like to calculate CSF volume separately for left and right hemispheres. In aseg.stats file I have volumes for 3rd, 4th and 5th ventricles as a whole. Is there any possibility to get volume values for right/left parts of 3rd, 4th and 5th ventricles? Thank you, Tanja. ___ 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] volume of CSF for hemispheres
Hi Tanja we don't do this by default, but I guess you could use the Talairach x coordinate to try to differentiate. cheers Bruce On Wed, 16 Feb 2011, Tetiana Dadakova wrote: > Dear list, > > I would like to calculate CSF volume separately for left and right > hemispheres. In aseg.stats file I have volumes for 3rd, 4th and 5th > ventricles as a whole. > Is there any possibility to get volume values for right/left parts of > 3rd, 4th and 5th ventricles? > > Thank you, > Tanja. > ___ > 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.
Re: [Freesurfer] volume of CSF for hemispheres
Thank you, Bruce. Could you recommend me any tutorial on this? Or probably can you just mention some steps or commands, where I should insert coordinates? Tanja. On Wed, Feb 16, 2011 at 3:15 PM, Bruce Fischl wrote: > Hi Tanja > > we don't do this by default, but I guess you could use the Talairach x > coordinate to try to differentiate. > > cheers > Bruce > On Wed, 16 Feb 2011, Tetiana Dadakova wrote: > >> Dear list, >> >> I would like to calculate CSF volume separately for left and right >> hemispheres. In aseg.stats file I have volumes for 3rd, 4th and 5th >> ventricles as a whole. >> Is there any possibility to get volume values for right/left parts of >> 3rd, 4th and 5th ventricles? >> >> Thank you, >> Tanja. >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] volume of CSF for hemispheres
Hi Tanja, I think Doug just put up a coordinate tutorial. For each voxel in the aseg label you are interested, compute it's tal coords and if the x is negative assign it to one pool and if it is positive assign it to the other cheers Bruce On Wed, 16 Feb 2011, Tetiana Dadakova wrote: > Thank you, Bruce. > > Could you recommend me any tutorial on this? Or probably can you just > mention some steps or commands, where I should insert coordinates? > > Tanja. > > > On Wed, Feb 16, 2011 at 3:15 PM, Bruce Fischl > wrote: >> Hi Tanja >> >> we don't do this by default, but I guess you could use the Talairach x >> coordinate to try to differentiate. >> >> cheers >> Bruce >> On Wed, 16 Feb 2011, Tetiana Dadakova wrote: >> >>> Dear list, >>> >>> I would like to calculate CSF volume separately for left and right >>> hemispheres. In aseg.stats file I have volumes for 3rd, 4th and 5th >>> ventricles as a whole. >>> Is there any possibility to get volume values for right/left parts of >>> 3rd, 4th and 5th ventricles? >>> >>> Thank you, >>> Tanja. >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] output of mris_anatomical_stats
Dear all, In mris_anatomical_stats, the "average cortical thickness" value comes with a measure of dispersion around the mean. Is this Standard Deviation? If so, is there a way to plot the 95% confidence intervals instead? Thanks, Marco _ Marco L. Loggia, PhD Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital Harvard Medical School CNY Building 120, suite 101E Charlestown, Massachusetts 02129 Phone: (617) 643-7267 Fax: (617) 643-7340 ma...@nmr.mgh.harvard.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.
Re: [Freesurfer] (no subject)
Cara Angela, La maggioranza degli utenti di questa mailing list (incluso il team di freesurfer, che mi ha chiesto di risponderti) non parla italiano. Per comunicazioni future ti suggerirei di scrivere in inglese, in modo da assicurarti assistenza diretta dal team. Per preprocessare i tuoi dati devi seguire questi step: 1) Utilizzando il comando 'setenv' devi specificare il path completo della directory contenente i tuoi soggetti. Per esempio, se la tua directory si trova in /DATI/SOGGETTI, devi usare il comando: setenv SUBJECTS_DIR /DATI/SOGGETTI 2) cd $SUBJECTS_DIR 3) mkdir -p NOMESOGGETTO/mri/orig 4) mri_convert FILE_NAME.nii NOMESOGGETTO/mri/orig/001.mgz 5) recon-all -s NOMESOGGETTO -autorecon-all Questo dovrebbe funzionare. In bocca al lupo! Marco _ Marco L. Loggia, PhD Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital Harvard Medical School CNY Building 120, suite 101E Charlestown, Massachusetts 02129 Phone: (617) 643-7267 Fax: (617) 643-7340 ma...@nmr.mgh.harvard.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.
Re: [Freesurfer] output of mris_anatomical_stats
Hi Marco that is the spatial standard deviation, which probably isn't a very interesting #. Typically the more interesting variance is cross subject. cheers Bruce On Wed, 16 Feb 2011, Marco Loggia, PhD wrote: > Dear all, > > > > In mris_anatomical_stats, the "average cortical thickness" value comes with > a measure of dispersion around the mean. Is this Standard Deviation? If so, > is there a way to plot the 95% confidence intervals instead? > > > > Thanks, > > Marco > > > > > _ > > > > Marco L. Loggia, PhD > > Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital > > Harvard Medical School > > > > CNY Building 120, suite 101E > > Charlestown, Massachusetts 02129 > > Phone: (617) 643-7267 > > Fax: (617) 643-7340 ma...@nmr.mgh.harvard.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.
Re: [Freesurfer] retinotopy manual?
Hi Doug, Sorry for the dumb beginner question, but to view the results projected onto their own anatomy, do I have to do anything special to their high res structural scan(like do a recon-all) ? Thanks. Michelle Quoting Douglas N Greve : > I don't have a formal manual yet (working on it). Below are a list of > steps that you need to run. The version 5 retinotopy stream is now > integrated with the rest of FSFAST, which is documented here: > http://nmr.mgh.harvard.edu/~greve/fsfast.intro.ppt > > doug > > 1. Create retinotopy paradigm file in each run directory, eg, > session/bold/001/rtopy.par > session/bold/002/rtopy.par etc > > This text file identifies the data in the directory in terms of the > stimulus type (polar or eccen) and the direction (pos or neg). Its > contents should look somethign like: > >stimtype polar >direction pos > > 2. Run preprocessing > > preproc-sess -surface self lhrh -fwhm 5 > > 3. Create analysis (30 sec period, 'rtopy.par' is the name of the > paradigm file from above): > > mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 \ >-retinotopy 30 -paradigm rtopy.par > mkanalysis-sess -a rtopy.self.rh -surface self rh -TR 2 \ >-retinotopy 30 -paradigm rtopy.par > > 4. Run analysis > > selxavg3-sess -a rtopy.self.lh -sf ... > selxavg3-sess -a rtopy.self.rh -sf ... > fieldsign-sess -a rtopy.self.lh -occip -sf ... > fieldsign-sess -a rtopy.self.rh -occip -sf ... > > 5. View results > a. Significance maps: > tksurfer-sess -a rtopy.self.lh -s sessid > b. Display raw angle > tksurfer-sess -a rtopy.self.lh -s sessid -map angle > c. Display angle masked by by sig > tksurfer-sess -a rtopy.self.lh -s sessid -map angle.masked > d. Display field sign > tksurfer-sess -a rtopy.self.lh -s sessid -fieldsign > > > > > > Michelle Umali wrote: >> Dear All, >> I was wondering if anyone knows of a step-by-step guide on how to do >> retinotopic analysis with freesurfer. >> >> Thanks. >> Michelle >> ___ >> 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: 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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] output of mris_anatomical_stats
Thanks Bruce for your prompt reply. The surfaces I feed to mris_anatomical_stats are actually not thickness data, but quantitative CBF maps, calculated using arterial spin labeling. I am trying to extract, for each subject, the average CBF value across the whole cortical surface. Considering this, the dispersion should be the SD of the CBF across all vertices, right? Is it not possible to obtain 95% C.I. instead of the SD? Marco _ Marco L. Loggia, PhD Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital Harvard Medical School CNY Building 120, suite 101E Charlestown, Massachusetts 02129 Phone: (617) 643-7267 Fax: (617) 643-7340 ma...@nmr.mgh.harvard.edu -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Wednesday, February 16, 2011 11:52 AM To: Marco Loggia, PhD Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] output of mris_anatomical_stats Hi Marco that is the spatial standard deviation, which probably isn't a very interesting #. Typically the more interesting variance is cross subject. cheers Bruce On Wed, 16 Feb 2011, Marco Loggia, PhD wrote: > Dear all, > > > > In mris_anatomical_stats, the "average cortical thickness" value comes > with a measure of dispersion around the mean. Is this Standard > Deviation? If so, is there a way to plot the 95% confidence intervals instead? > > > > Thanks, > > Marco > > > > > _ > > > > Marco L. Loggia, PhD > > Postdoctoral Fellow, Mass General Hospital & Brigham and Women's > Hospital > > Harvard Medical School > > > > CNY Building 120, suite 101E > > Charlestown, Massachusetts 02129 > > Phone: (617) 643-7267 > > Fax: (617) 643-7340 ma...@nmr.mgh.harvard.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.
Re: [Freesurfer] FS 5.1
Hi, For what it's worth, I have seen a very similar skull-strip failure on at least one of my brains processed with Freesurfer 5.0 but not using the -nuintensitycor-3T flag. Happy to send data, if helpful. Best. Michael On Wed, Feb 16, 2011 at 2:03 PM, Mehul Sampat wrote: > Hi Bruce, > > Okay. I will try it out 5.1 in the future and compare it to 4.5. > > I also have a question about comparisons between version 4.5 and 5.0 > > In some cases, I saw that FS 4.5 does a slightly better job at skull > stripping than FS 5.0. > Esentially, FS 5.0 seems to make errors in the back of the brain and cuts > out some tissue. > (Please see attached images). > > The images are the same slice from the same subject processed with FS 4.5 > and 5.0 (This happens across 5-10 slices) > In 5.0, I used the following command: recon-all -s "subj--id" -i > "nifti-file" -all -nuintensitycor-3T > (I have seen this issue in atleast 5 subjects in our data) > > Since 5.0 uses the graph cuts, could the error be due the combination of > (graph cuts + -nuintensitycor-3T) ? > Also, I guess I could run 5.0 and use only graph cuts or -nuintensitycor-3T > to isolate the error ? > > Thanks > Mehul > > > > On Tue, Feb 15, 2011 at 12:05 PM, Bruce Fischl > wrote: >> >> Hi Mehul, >> >> I think 5.1 will work better for large ventricles than 4.5, but I'll be >> interested to hear your experience. >> >> cheers >> Bruce >> On Tue, 15 Feb 2011, Mehul Sampat wrote: >> >>> Hi Bruce, >>> We have two studies being conducted (one cross-sectional and one >>> longitudinal) >>> Some of the subjects in have a lot of atrophy and have large ventircles. >>> >>> For the cross-sectional analysis stream are there many differences >>> between >>> 4.5 and the forthcoming 5.1 ? Or would it be fine to use 4.5 for >>> cross-sectional analysis ? >>> >>> (I understand that for the longitudinal study, I should wait for 5.1 and >>> process all the timepoints with 5.1) >>> >>> >>> Thanks >>> Mehul >>> >>> >>> >>> On Thu, Jan 20, 2011 at 10:36 AM, Bruce Fischl >>> wrote: >>> Hi Derin we are tracking down some issues with it and hope to have it out within a month cheers Bruce On Thu, 20 Jan 2011, Derin Cobia wrote: > All, > > Just curious about the current estimated timeline for version 5.1, > trying to schedule some projects around it. Thanks! > > -Derin > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. >>> > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FS 5.1
you can try the -no-gcut flag at the end of recon-all to disable the gcut stage within skullstrip. for the next release (5.1), gcut is being made more conservative to reduce these failures. n. On Wed, 2011-02-16 at 14:30 -0500, Michael Waskom wrote: > Hi, > > For what it's worth, I have seen a very similar skull-strip failure on > at least one of my brains processed with Freesurfer 5.0 but not using > the -nuintensitycor-3T flag. Happy to send data, if helpful. > > Best. > Michael > > On Wed, Feb 16, 2011 at 2:03 PM, Mehul Sampat wrote: > > Hi Bruce, > > > > Okay. I will try it out 5.1 in the future and compare it to 4.5. > > > > I also have a question about comparisons between version 4.5 and 5.0 > > > > In some cases, I saw that FS 4.5 does a slightly better job at skull > > stripping than FS 5.0. > > Esentially, FS 5.0 seems to make errors in the back of the brain and cuts > > out some tissue. > > (Please see attached images). > > > > The images are the same slice from the same subject processed with FS 4.5 > > and 5.0 (This happens across 5-10 slices) > > In 5.0, I used the following command: recon-all -s "subj--id" -i > > "nifti-file" -all -nuintensitycor-3T > > (I have seen this issue in atleast 5 subjects in our data) > > > > Since 5.0 uses the graph cuts, could the error be due the combination of > > (graph cuts + -nuintensitycor-3T) ? > > Also, I guess I could run 5.0 and use only graph cuts or -nuintensitycor-3T > > to isolate the error ? > > > > Thanks > > Mehul > > > > > > > > On Tue, Feb 15, 2011 at 12:05 PM, Bruce Fischl > > wrote: > >> > >> Hi Mehul, > >> > >> I think 5.1 will work better for large ventricles than 4.5, but I'll be > >> interested to hear your experience. > >> > >> cheers > >> Bruce > >> On Tue, 15 Feb 2011, Mehul Sampat wrote: > >> > >>> Hi Bruce, > >>> We have two studies being conducted (one cross-sectional and one > >>> longitudinal) > >>> Some of the subjects in have a lot of atrophy and have large ventircles. > >>> > >>> For the cross-sectional analysis stream are there many differences > >>> between > >>> 4.5 and the forthcoming 5.1 ? Or would it be fine to use 4.5 for > >>> cross-sectional analysis ? > >>> > >>> (I understand that for the longitudinal study, I should wait for 5.1 and > >>> process all the timepoints with 5.1) > >>> > >>> > >>> Thanks > >>> Mehul > >>> > >>> > >>> > >>> On Thu, Jan 20, 2011 at 10:36 AM, Bruce Fischl > >>> wrote: > >>> > Hi Derin > > we are tracking down some issues with it and hope to have it out within > a > month > > cheers > Bruce > On Thu, 20 Jan 2011, Derin Cobia wrote: > > > All, > > > > Just curious about the current estimated timeline for version 5.1, > > trying > > to schedule some projects around it. Thanks! > > > > -Derin > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom > it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you > in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > >>> > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > The information in this e-mail is intended only for the person to whom it is > > addressed. If you believe this e-mail was sent to you in error and the > > e-mail > > contains patient information, please contact the Partners Compliance > > HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to you in > > error > > but does not contain patient information, please contact the sender and > > properly > > dispose of the e-mail. > > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] question regarding T1-data quality
the surfaces look ok, although the data looks pretty low contrast. Was it a flash scan? what is the voxel resolution? On Wed, 16 Feb 2011, Eveline Geiser wrote: > Dear List, > we recorded this anatomical data on a clinical scanner (Philips Achieva 3T) > with the following parameters: eight-channel sense head coil, TE 2.3 ms TR = > 20ms, angle = 20degree. > do you think it is usable? > thanks for your reply > > ___ 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] Between Task Analysis
Thank you for your response! We decided to run an isxconcat-sess on both analyses (day1 and day2), and we used fscalc to do day1 - day2. Now we're trying to run mri_glmfit. However, the FSGD files we used before either specified day1 or day2 sessions. How do we create an FSGD file now that each data point is actually 'day1 - day2' for one subject and not one of the pre-existing subject folders? Thanks! --Mandy Nagy On Tue, Feb 15, 2011 at 5:12 PM, Douglas N Greve wrote: > In principle you can do it either way and get the same result. From a > practical standpoint, it is probably easier to do the day2-day1 subtraction, > then do the group analysis. > > doug > > Mandy Nagy wrote: >> >> Hi all, >> >> We are attempting to do an analysis for subjects that came in on two >> different days to perform two similar but different tasks (one >> learning condition, one control). Each of the tasks is structured >> such that there are 30sec rest epochs alternating with 30sec active >> (typing) epochs for a total of 12.5 minutes (the task begins and ends >> with rest). We are trying to compare the typing period for the >> control task to the typing period for the learning task. >> >> We currently have first-level analyses of each of the tasks (active >> condition vs. null rest condition). Can we do within-subject >> comparisons and then do a group analysis on those? Or did we need to >> concatenate the learning and control conditions in the first-level >> analysis? If that is the case, how would you suggest that we do this? >> >> Paradigm file: >> >> 0 0 30 1 Rest >> 30 1 30 1 Typing >> 60 0 30 1 Rest >> 90 1 30 1 Typing >> 120 0 30 1 Rest >> 150 1 30 1 Typing >> 180 0 30 1 Rest >> 210 1 30 1 Typing >> 240 0 30 1 Rest >> 270 1 30 1 Typing >> 300 0 30 1 Rest >> 330 1 30 1 Typing >> 360 0 30 1 Rest >> 390 1 30 1 Typing >> 420 0 30 1 Rest >> 450 1 30 1 Typing >> 480 0 30 1 Rest >> 510 1 30 1 Typing >> 540 0 30 1 Rest >> 570 1 30 1 Typing >> 600 0 30 1 Rest >> 630 1 30 1 Typing >> 660 0 30 1 Rest >> 690 1 30 1 Typing >> 720 0 30 1 Rest >> >> >> Thanks in advance! >> --Mandy Nagy >> ___ >> 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: 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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] retinotopy manual?
Yes, you need to run recon-all in order to run the FSFAST analysis. doug Michelle Umali wrote: > Hi Doug, > Sorry for the dumb beginner question, but to view the results > projected onto their own anatomy, do I have to do anything special to > their high res structural scan(like do a recon-all) ? > > Thanks. > Michelle > > > Quoting Douglas N Greve : > >> I don't have a formal manual yet (working on it). Below are a list of >> steps that you need to run. The version 5 retinotopy stream is now >> integrated with the rest of FSFAST, which is documented here: >> http://nmr.mgh.harvard.edu/~greve/fsfast.intro.ppt >> >> doug >> >> 1. Create retinotopy paradigm file in each run directory, eg, >> session/bold/001/rtopy.par >> session/bold/002/rtopy.par etc >> >> This text file identifies the data in the directory in terms of the >> stimulus type (polar or eccen) and the direction (pos or neg). Its >> contents should look somethign like: >> >>stimtype polar >>direction pos >> >> 2. Run preprocessing >> >> preproc-sess -surface self lhrh -fwhm 5 >> >> 3. Create analysis (30 sec period, 'rtopy.par' is the name of the >> paradigm file from above): >> >> mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 \ >>-retinotopy 30 -paradigm rtopy.par >> mkanalysis-sess -a rtopy.self.rh -surface self rh -TR 2 \ >>-retinotopy 30 -paradigm rtopy.par >> >> 4. Run analysis >> >> selxavg3-sess -a rtopy.self.lh -sf ... >> selxavg3-sess -a rtopy.self.rh -sf ... >> fieldsign-sess -a rtopy.self.lh -occip -sf ... >> fieldsign-sess -a rtopy.self.rh -occip -sf ... >> >> 5. View results >> a. Significance maps: >> tksurfer-sess -a rtopy.self.lh -s sessid >> b. Display raw angle >> tksurfer-sess -a rtopy.self.lh -s sessid -map angle >> c. Display angle masked by by sig >> tksurfer-sess -a rtopy.self.lh -s sessid -map angle.masked >> d. Display field sign >> tksurfer-sess -a rtopy.self.lh -s sessid -fieldsign >> >> >> >> >> >> Michelle Umali wrote: >>> Dear All, >>> I was wondering if anyone knows of a step-by-step guide on how to do >>> retinotopic analysis with freesurfer. >>> >>> Thanks. >>> Michelle >>> ___ >>> 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: 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. > > > > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Between Task Analysis
You mean you have used the day1 recon-all with the day1 functional (and same for day 2)? I would probably pick an anatomical from one day and use them with the functionals for both days. You can use either FSGD file assuming that the class membership and continuous variables are the same. If you're just doing an OSGM, then you don't even need a an FSGD file (but it does not hurt). doug Mandy Nagy wrote: > Thank you for your response! > > We decided to run an isxconcat-sess on both analyses (day1 and day2), > and we used fscalc to do day1 - day2. Now we're trying to run > mri_glmfit. However, the FSGD files we used before either specified > day1 or day2 sessions. How do we create an FSGD file now that each > data point is actually 'day1 - day2' for one subject and not one of > the pre-existing subject folders? > > Thanks! > --Mandy Nagy > > On Tue, Feb 15, 2011 at 5:12 PM, Douglas N Greve > wrote: > >> In principle you can do it either way and get the same result. From a >> practical standpoint, it is probably easier to do the day2-day1 subtraction, >> then do the group analysis. >> >> doug >> >> Mandy Nagy wrote: >> >>> Hi all, >>> >>> We are attempting to do an analysis for subjects that came in on two >>> different days to perform two similar but different tasks (one >>> learning condition, one control). Each of the tasks is structured >>> such that there are 30sec rest epochs alternating with 30sec active >>> (typing) epochs for a total of 12.5 minutes (the task begins and ends >>> with rest). We are trying to compare the typing period for the >>> control task to the typing period for the learning task. >>> >>> We currently have first-level analyses of each of the tasks (active >>> condition vs. null rest condition). Can we do within-subject >>> comparisons and then do a group analysis on those? Or did we need to >>> concatenate the learning and control conditions in the first-level >>> analysis? If that is the case, how would you suggest that we do this? >>> >>> Paradigm file: >>> >>> 0 0 30 1 Rest >>> 30 1 30 1 Typing >>> 60 0 30 1 Rest >>> 90 1 30 1 Typing >>> 120 0 30 1 Rest >>> 150 1 30 1 Typing >>> 180 0 30 1 Rest >>> 210 1 30 1 Typing >>> 240 0 30 1 Rest >>> 270 1 30 1 Typing >>> 300 0 30 1 Rest >>> 330 1 30 1 Typing >>> 360 0 30 1 Rest >>> 390 1 30 1 Typing >>> 420 0 30 1 Rest >>> 450 1 30 1 Typing >>> 480 0 30 1 Rest >>> 510 1 30 1 Typing >>> 540 0 30 1 Rest >>> 570 1 30 1 Typing >>> 600 0 30 1 Rest >>> 630 1 30 1 Typing >>> 660 0 30 1 Rest >>> 690 1 30 1 Typing >>> 720 0 30 1 Rest >>> >>> >>> Thanks in advance! >>> --Mandy Nagy >>> ___ >>> 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: 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. >> >> >> > > > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] output of mris_anatomical_stats
Hi Marco, no, there's not a way to get 95% conf intervals out of it. sorry, doug Marco Loggia, PhD wrote: > Thanks Bruce for your prompt reply. > > The surfaces I feed to mris_anatomical_stats are actually not thickness > data, but quantitative CBF maps, calculated using arterial spin labeling. > > I am trying to extract, for each subject, the average CBF value across the > whole cortical surface. Considering this, the dispersion should be the SD of > the CBF across all vertices, right? > > Is it not possible to obtain 95% C.I. instead of the SD? > > Marco > > _ > > Marco L. Loggia, PhD > Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital > Harvard Medical School > > CNY Building 120, suite 101E > Charlestown, Massachusetts 02129 > Phone: (617) 643-7267 > Fax: (617) 643-7340 ma...@nmr.mgh.harvard.edu > > > -Original Message- > From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] > Sent: Wednesday, February 16, 2011 11:52 AM > To: Marco Loggia, PhD > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] output of mris_anatomical_stats > > Hi Marco > > that is the spatial standard deviation, which probably isn't a very > interesting #. Typically the more interesting variance is cross subject. > > cheers > Bruce > > > On Wed, 16 Feb 2011, Marco > Loggia, PhD wrote: > > >> Dear all, >> >> >> >> In mris_anatomical_stats, the "average cortical thickness" value comes >> with a measure of dispersion around the mean. Is this Standard >> Deviation? If so, is there a way to plot the 95% confidence intervals >> > instead? > >> >> Thanks, >> >> Marco >> >> >> >> >> _ >> >> >> >> Marco L. Loggia, PhD >> >> Postdoctoral Fellow, Mass General Hospital & Brigham and Women's >> Hospital >> >> Harvard Medical School >> >> >> >> CNY Building 120, suite 101E >> >> Charlestown, Massachusetts 02129 >> >> Phone: (617) 643-7267 >> >> Fax: (617) 643-7340 ma...@nmr.mgh.harvard.edu >> >> >> > > > > ___ > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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.
