Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Cerebellum segmentation, auto vs manual reference?
by McLean John (NHS Greater Glasgow & Clyde) 13 May '11

13 May '11

Hi, I've found some volume differences in the cerebellum between two groups I've been studying. I used freesurfer v4.5 to do the segmentation. I am looking for a reference to justify the use of Freesurfer and to say that it compares well with manual tracing of the cerebellum but I'm struggling to find a paper with that data. Can anyone comment or point me in the right direction? The Fischl et al 2002 Neuron paper has a comparison of most subcortical regions but doesn't include the cerebellum and other papers I've seen by Makris et al 03' and 05' looks to employ a more involved and detailed approach for the cerebellum rather than only running Freesurfer's recon-all process. Many Thanks John ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients NHSmail provides an email address for your career in the NHS and can be accessed anywhere For more information and to find out how you can switch, visit www.connectingforhealth.nhs.uk/nhsmail ********************************************************************************************************************

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Re: [Freesurfer] Pial surface error
by Allie Rosen 13 May '11

13 May '11

Hi Mario, I'm not sure what an N4 correction is, but the Freesurfer team helped me to solve the problem. Here are their instructions: Sometimes when the skullstrip is wrong, it affects the surfaces even if the wm parcellation is correct. I ran -skullstrip with the watershed parameter of 30, and then reran the subject with -autorecon2 -autorecon3. You can find info how how to run watershed here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix <http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix>I hope this helps! I can send over our full conversation if this doesn't give you the information you need. Allie On Fri, May 13, 2011 at 4:26 PM, Mario Ortega <mario.ortega(a)gmail.com>wrote: > HI Allie, > I am having this exact issue, and I was able to fix only a few of them, Did > the Freesurfer team ever give you a reliable fix? I used an N4 correction > before the entire FS process. > -Mario > > > On Wed, Apr 20, 2011 at 8:32 AM, Allie Rosen <rosen.allie(a)gmail.com>wrote: > >> Hi, >> >> Do you want me to email you in a few days about this? >> >> Allie >> >> >> >> >> On Tue, Apr 19, 2011 at 10:25 AM, Khoa Nguyen <khoa(a)nmr.mgh.harvard.edu>wrote: >> >>> Got it. I'll look at it and get back to you. >>> >>> >>> On Tue, 19 Apr 2011, Allie Rosen wrote: >>> >>> Hi, >>>> >>>> http://dl.dropbox.com/u/14127241/C42.tar.gz >>>> >>>> Here is the link to the subject. I hope this works!! >>>> >>>> Allie >>>> >>>> >>>> >>>> On Tue, Apr 19, 2011 at 9:38 AM, Khoa Nguyen <khoa(a)nmr.mgh.harvard.edu >>>> >wrote: >>>> >>>> Another way you can try is upload it to your google doc account and >>>>> send me >>>>> the link. Someone did that before. >>>>> >>>>> >>>>> On Tue, 19 Apr 2011, Allie Rosen wrote: >>>>> >>>>> Hi, >>>>> >>>>>> >>>>>> No, I'm not from the centre. I'm working on putting the files in >>>>>> Dropbox >>>>>> and >>>>>> sending you a link to them, because apparently I don't have ftp >>>>>> access. >>>>>> >>>>>> Allie >>>>>> >>>>>> >>>>>> >>>>>> On Tue, Apr 19, 2011 at 8:37 AM, Khoa Nguyen < >>>>>> khoa(a)nmr.mgh.harvard.edu >>>>>> >>>>>>> wrote: >>>>>>> >>>>>> >>>>>> Are you from the center? If so you can just cd into /space/outgoing >>>>>> and >>>>>> >>>>>>> copy your file there. If not, you can follow the instructions in the >>>>>>> box >>>>>>> at >>>>>>> the top using a terminal. >>>>>>> >>>>>>> >>>>>>> On Tue, 19 Apr 2011, Allie Rosen wrote: >>>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> >>>>>>>> I'm really sorry, but I don't understand those instructions. Do I >>>>>>>> login >>>>>>>> to >>>>>>>> the freesurfer website? Or do I login through a terminal somehow? Do >>>>>>>> I >>>>>>>> type >>>>>>>> the stuff in the boxes into the terminal? >>>>>>>> >>>>>>>> Thanks, >>>>>>>> Allie >>>>>>>> >>>>>>>> >>>>>>>> On Tue, Apr 19, 2011 at 8:18 AM, Khoa Nguyen < >>>>>>>> khoa(a)nmr.mgh.harvard.edu >>>>>>>> >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> >>>>>>>> Hi Allie, >>>>>>>> >>>>>>>> >>>>>>>>> You can compress the subject dir and upload it following the >>>>>>>>> instructions >>>>>>>>> here >>>>>>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> On Tue, 19 Apr 2011, Allie Rosen wrote: >>>>>>>>> >>>>>>>>> Hi Khoa, >>>>>>>>> >>>>>>>>> >>>>>>>>> How do I upload subjects? >>>>>>>>>> >>>>>>>>>> Thanks, >>>>>>>>>> Allie >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Tue, Apr 19, 2011 at 8:06 AM, Khoa Nguyen < >>>>>>>>>> khoa(a)nmr.mgh.harvard.edu >>>>>>>>>> >>>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Hi Allie, >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Can you upload the subject? I'll take a look and see if I can >>>>>>>>>>> figure >>>>>>>>>>> out >>>>>>>>>>> what's wrong. >>>>>>>>>>> >>>>>>>>>>> -Khoa >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Tue, 19 Apr 2011, Allie Rosen wrote: >>>>>>>>>>> >>>>>>>>>>> Hi, >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> This (recon-all after wm.mgz and brainmask.mgz edits) didn't >>>>>>>>>>> work. >>>>>>>>>>> >>>>>>>>>>>> The >>>>>>>>>>>> part >>>>>>>>>>>> that wasn't included in the pial or white matter surfaces is >>>>>>>>>>>> still >>>>>>>>>>>> not >>>>>>>>>>>> included. The intensities in the white matter regions are no >>>>>>>>>>>> different >>>>>>>>>>>> than >>>>>>>>>>>> in white matter regions that were included in the white matter. >>>>>>>>>>>> Any >>>>>>>>>>>> other >>>>>>>>>>>> suggestions? >>>>>>>>>>>> >>>>>>>>>>>> Thanks, >>>>>>>>>>>> Allie >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> On Mon, Apr 18, 2011 at 7:53 PM, Allie Rosen < >>>>>>>>>>>> rosen.allie(a)gmail.com >>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> wrote: >>>>>>>>>>>> >>>>>>>>>>>> Hi Bruce, >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> I am running recon-all tonight using wm voxels that I manually >>>>>>>>>>>> >>>>>>>>>>>>> added >>>>>>>>>>>>> (I >>>>>>>>>>>>> also edited brainmask.mgz to add missing grey matter). To me it >>>>>>>>>>>>> doesn't >>>>>>>>>>>>> really look like a case of the white matter not having a high >>>>>>>>>>>>> enough >>>>>>>>>>>>> intensity. It simply looks like the whole lobe was ignored, >>>>>>>>>>>>> regardless >>>>>>>>>>>>> of >>>>>>>>>>>>> intensity. But I'll check tomorrow to see if the intensity is >>>>>>>>>>>>> low. >>>>>>>>>>>>> >>>>>>>>>>>>> Thanks, >>>>>>>>>>>>> Allie >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> On Mon, Apr 18, 2011 at 7:38 PM, Bruce Fischl < >>>>>>>>>>>>> fischl(a)nmr.mgh.harvard.edu>wrote: >>>>>>>>>>>>> >>>>>>>>>>>>> What is the intensity of the white matter in the regions you >>>>>>>>>>>>> drew >>>>>>>>>>>>> in? >>>>>>>>>>>>> A >>>>>>>>>>>>> >>>>>>>>>>>>> couple of control points might help if it is less than 110 >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Apr 18, 2011, at 12:36 PM, Allie Rosen < >>>>>>>>>>>>>> rosen.allie(a)gmail.com> >>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>> Hi Sita, >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thanks for all the responses! I've actually had the same >>>>>>>>>>>>>> problem >>>>>>>>>>>>>> for >>>>>>>>>>>>>> multiple subjects. I'm using version 5.0.0. I'll try fixing >>>>>>>>>>>>>> the >>>>>>>>>>>>>> cerebellum >>>>>>>>>>>>>> as well. I've attached pictures of where I am adding wm >>>>>>>>>>>>>> voxels. >>>>>>>>>>>>>> They >>>>>>>>>>>>>> aren't >>>>>>>>>>>>>> really in the same places as in the online tutorials. Could >>>>>>>>>>>>>> you >>>>>>>>>>>>>> take >>>>>>>>>>>>>> a >>>>>>>>>>>>>> quick >>>>>>>>>>>>>> look to see if they're in the right place? >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>> Allie >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Mon, Apr 18, 2011 at 12:31 PM, Sita Kakunoori << >>>>>>>>>>>>>> sita(a)nmr.mgh.harvard.edu> >>>>>>>>>>>>>> sita(a)nmr.mgh.harvard.edu> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> Hi Allie, >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> pial surface which looks like this can only be corrected by >>>>>>>>>>>>>>> correcting >>>>>>>>>>>>>>> the wm.mgz. Also I would suggest to try and fix the >>>>>>>>>>>>>>> cerebellum >>>>>>>>>>>>>>> and >>>>>>>>>>>>>>> see >>>>>>>>>>>>>>> if it >>>>>>>>>>>>>>> corrects the surfaces as well. Since part of the cerebellum >>>>>>>>>>>>>>> is >>>>>>>>>>>>>>> stripped >>>>>>>>>>>>>>> off, >>>>>>>>>>>>>>> it's probably affecting the segmentation as well but I could >>>>>>>>>>>>>>> be >>>>>>>>>>>>>>> wrong. >>>>>>>>>>>>>>> what >>>>>>>>>>>>>>> version of freesurfer are you using. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Sita. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Mon, 18 Apr 2011, Allie Rosen wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi Sita, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Can I still add voxels to wm.mgz even though the points >>>>>>>>>>>>>>> would be >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> outside >>>>>>>>>>>>>>>> even the pial boundary? >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>> Allie >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On Mon, Apr 18, 2011 at 12:18 PM, Sita Kakunoori >>>>>>>>>>>>>>>> < <sita(a)nmr.mgh.harvard.edu>sita(a)nmr.mgh.harvard.edu>wrote: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi Allie, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> This probably needs white matter edits but it's hard to >>>>>>>>>>>>>>>> tell >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> from >>>>>>>>>>>>>>>>> one >>>>>>>>>>>>>>>>> slice. Please refer to our white matter edits wiki and >>>>>>>>>>>>>>>>> toplogical >>>>>>>>>>>>>>>>> defects >>>>>>>>>>>>>>>>> wiki and see if it helps in fixing the errors in your >>>>>>>>>>>>>>>>> datasets. >>>>>>>>>>>>>>>>> Also >>>>>>>>>>>>>>>>> it >>>>>>>>>>>>>>>>> looks like part of the Cerebellum is stripped off. You >>>>>>>>>>>>>>>>> might >>>>>>>>>>>>>>>>> want >>>>>>>>>>>>>>>>> to >>>>>>>>>>>>>>>>> correct >>>>>>>>>>>>>>>>> that as well. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> < >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> < >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Sita. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> On Mon, 18 Apr 2011, Allie Rosen wrote: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Once processed, several of my subjects have had errors >>>>>>>>>>>>>>>>> around >>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> occipital >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> lobe. Attached is an example. I've already tried editing >>>>>>>>>>>>>>>>>> brainmask.mgz >>>>>>>>>>>>>>>>>> and >>>>>>>>>>>>>>>>>> running recon-all, but as you can see, this didn't change >>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>> pial >>>>>>>>>>>>>>>>>> or >>>>>>>>>>>>>>>>>> wm >>>>>>>>>>>>>>>>>> borders. What can I do to fix this? >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>> Allie Rosen, MSc Candidate >>>>>>>>>>>>>>>>>> Graduate Student, Department of Neurosurgery >>>>>>>>>>>>>>>>>> Toronto Western Hospital 14-327 >>>>>>>>>>>>>>>>>> 399 Bathurst St. >>>>>>>>>>>>>>>>>> University of Toronto >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> The information in this e-mail is intended only for the >>>>>>>>>>>>>>>>>> person >>>>>>>>>>>>>>>>>> to >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> whom >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> it >>>>>>>>>>>>>>>>> is >>>>>>>>>>>>>>>>> addressed. If you believe this e-mail was sent to you in >>>>>>>>>>>>>>>>> error >>>>>>>>>>>>>>>>> and >>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>> e-mail >>>>>>>>>>>>>>>>> contains patient information, please contact the Partners >>>>>>>>>>>>>>>>> Compliance >>>>>>>>>>>>>>>>> HelpLine at >>>>>>>>>>>>>>>>> <http://www.partners.org/complianceline> >>>>>>>>>>>>>>>>> http://www.partners.org/complianceline . If the e-mail was >>>>>>>>>>>>>>>>> sent >>>>>>>>>>>>>>>>> to >>>>>>>>>>>>>>>>> you >>>>>>>>>>>>>>>>> in >>>>>>>>>>>>>>>>> error >>>>>>>>>>>>>>>>> but does not contain patient information, please contact >>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>> sender >>>>>>>>>>>>>>>>> and >>>>>>>>>>>>>>>>> properly >>>>>>>>>>>>>>>>> dispose of the e-mail. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> <2.png> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> <3.png> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>> Freesurfer mailing list >>>>>>>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>> >>>>>>>> >>>>>> >>>> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >

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Re: [Freesurfer] Temporal lobe tracing abnomality uncorrected by control points
by Bruce Fischl 13 May '11

13 May '11

Hi Ammar, if you adjust control points you should be running autorecon2-cp not -wm. cheers Bruce On Fri, 13 May 2011, Moiyadi, Ammar wrote: > Hi I attached the log file for this subject. I tried adjusting control points and performing autorecon2-wm in repeated iterations. It helped a little but I still am missing a large chunk of both gray and white temporal matter. I'm not sure how many iterations it will take to get a complete tracing but it doesn't seem to be helping as much as the initial few runs. > > Ammar Moiyadi, BS > Professional Research Assistant > Psychiatry, School of Medicine > 303-724-5490 > ________________________________________ > From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] > Sent: Tuesday, May 10, 2011 6:01 PM > To: Moiyadi, Ammar > Subject: RE: [Freesurfer] Temporal lobe tracing abnomality uncorrected by control points > > can you send us the recon-all.log file for that subject? And make sure to > cc the list on your replies so others can help! > > Bruce > On Tue, 10 May 2011, > Moiyadi, Ammar wrote: > >> Hi Bruce - The image is of the brainmask.mgz file. I have attached another image showing the wm.mgz file - you're right, the wm regions where I placed the control groups is very dark if not absent. I still don't understand why the proper gray matter boundaries were not obtained however. I did run autorecon2-wm after adding the control points but I will run it again just in case. >> >> Thanks for your help, >> >> Ammar >> ________________________________________ >> From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] >> Sent: Tuesday, May 10, 2011 2:34 PM >> To: Moiyadi, Ammar >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Temporal lobe tracing abnomality uncorrected by control points >> >> what image are you displaying in this png? If it is one of the brain*.mgz >> then your control points aren't working as the wm is still very dark where >> you place them. Did you run autorecon2-wm after putting the control points >> in? >> >> On Tue, 10 May 2011, Moiyadi, >> Ammar wrote: >> >>> Dear Freesurfers, >>> >>> Freesurfer's autorecon is having trouble tracing both gray and white matter boundaries in the temporal region of one of my subjects (even after I added control points for the white matter). I have attached a png screen shot of this abnormality and was wondering if anyone has any ideas to correct this since I have never seen such a large tracing error before. >>> >>> Your input is much appreciated! >>> >>> Ammar >>> >> >> >> 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. >> >> >

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display results on fsaverage / calculate area
by Boris Bernhardt 13 May '11

13 May '11

Hello Freesurfer-experts, I just analyzed some FreeSurfer cortical thickness data that have been surface-resampled to fsaverage (using mris_surf2surf with -s fsaverage). For the visualization and reporting of my findings, I have a two questions: 1. Is there anything that conceptually speaks against showing my results on non-inflated surfaces of fsaverage, such as the white matter surface, the pial surface, or even a mid-surface model? 2. I have a couple of ROIs defined on the surface of fsaverage and want to report the surface area of a given ROI in mm^2. Should I calculate the area of a ROI directly from the given surface of fsaverage, or to take the area computations from ?h.pial.avg.area.mgh/?h.white.avg.area.mgh which represent the averages of the individuals that went into fsaverage. I am asking because I was slightly unclear of the wiki-instructions: https://surfer.nmr.mgh.harvard.edu/fswiki/GroupAverageSurface suggests to use ?h.pial.avg.area.mgh; on the other hand, the more recently edited http://surfer.nmr.mgh.harvard.edu/fswiki/FsAverage says that "The surface area of the new average subject (fsaverage) is that of a typical subject" I am using freesurfer 4.5.0. Hope my questions make sense and thank you very much for answering them, Boris --- Boris Bernhardt, PhD Max Planck Institute for Human Cognitive and Brain Sciences Stephanstr. 1a, 04103 Leipzig, Germany p: +(49) 341 9940 2658 e: bernhardt(a)cbs.mpg.de http://www.cbs.mpg.de/~bernhardt

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comparing FS version 4.0 and FS versione 5.2
by irene.mat＠libero.it 13 May '11

13 May '11

Hi all, I'm performing a follow-up longitudinal study in a group of patients. I have 2 brain MRIs per patient (T0 and T1 after 4 years). I'd like to know if I can analyse the T0 MRI with FS version 4.0 and compare these results with T1 MRI analyzed with FS version 5.2. Thanks, Irene Mattisi University Hospital of Padova, Italy.

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recon-all - problem with corRead(): can't open file */COR-.info
by Vanessa Lim 12 May '11

12 May '11

Hi, I have files from Siemen's Skyra which I have used MRI_Convert to nii I have tried using just the dicom files as well as changing the files to *.nii.gz but I still get the error corRead(): can't open file /home/virtualuser/apps/freesurfer/subjects/SPARSEG/COR-.info $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ I get files in G2 but there is nothing in the mri/orig I am following http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction as I am completely new to freesurfer. I'm using a virtual machine on Vista; Ubantu. Many thanks! Regards, Vanessa Error below: FreeSurfer:~/apps/freesurfer/subjects/GrossNii> recon-all -i ~/apps/freesurfer/subjects/SPARSEG -subjid G2 Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.0.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.0.0 INFO: SUBJECTS_DIR is /home/virtualuser/apps/freesurfer/subjects Actual FREESURFER_HOME /home/virtualuser/apps/freesurfer Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux /home/virtualuser/apps/freesurfer/subjects/G2 mri_convert /home/virtualuser/apps/freesurfer/subjects/SPARSEG /home/virtualuser/apps/freesurfer/subjects/G2/mri/orig/001.mgz mri_convert /home/virtualuser/apps/freesurfer/subjects/SPARSEG /home/virtualuser/apps/freesurfer/subjects/G2/mri/orig/001.mgz corRead(): can't open file /home/virtualuser/apps/freesurfer/subjects/SPARSEG/COR-.info $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /home/virtualuser/apps/freesurfer/subjects/SPARSEG... Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux

3 2

stop receiving emails
by Krista Kelly 12 May '11

12 May '11

How do I stop receiving emails from everyone asking and responding to questions about FreeSurfer?

2 1

Use of images
by Bruna Bressan Valentini 12 May '11

12 May '11

> I was invited to be co-author of a chapter of a new book on radiology. The chapter is about neuro anatomy and the main author is interested in using the images of the patients I have processed in FreeSurfer, to demonstrate the anatomy of the sulcs and gyri, as well as brain structures. I would like to know if that's permitted, since the program is used mainy in research. If so, how should I reference the FreeSurfer? Thanks, Bruna

1 0

tkmedit
by Michelle Umali 12 May '11

12 May '11

Dear Freesurfers, I've noticed some problems in some inflated brains with the curvature displayed that I know will require manual intervention: -random spots of abnormally intense green or very intense red -tiny protrusions -falx cerebri obscuring parietal region -subcallosal splotches of red-green I've been reading the troubleshooting webpages, but I am not sure what is causing the above issues. Any suggestions on the appropriate edits would be greatly appreciated. Thanks. Michelle

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Re: [Freesurfer] Interpreting results from Qdec
by Gallen, Courtney (NIH/NIDA) [F] 12 May '11

12 May '11

Thanks for the reply! I'm fairly certain that I'm using the same model. In Qdec: 2 discrete variables, 1 nuisance variable. In SPSS: a univariate ANOVA with 2 factors and 1 covariate. I understand the difference between Qdec and SPSS may be because Qdec looks at the entire cortex. Are there any realistic ways to work around this using something like SPSS? All I really want is to generate a figure with means for each of my groups, so I can understand what's driving the interaction. Any other suggestions about how to do so? -----Original Message----- From: greve(a)nmr.mgh.harvard.edu [mailto:greve@nmr.mgh.harvard.edu] Sent: Thursday, April 28, 2011 9:06 AM To: Gallen, Courtney (NIH/NIDA) [F] Subject: Re: [Freesurfer] Interpreting results from Qdec Hi Courtney, a couple of suggestions: 1. make sure that QDEC and SPSS are using the identical model. 2. make sure that the values that you are extracting the same as the input to QDEC/glmfit (eg, don't use thickness for one and volume for another). It is possible for the ROI analysis to give very different results, but it usually requires that you select the voxels based on an unsigned statistic (eg, an F-test). This opens the possibility that positives and negatives in the ROI sum to 0. doug > Thanks Jesse. This does sound very similar to my issue. > > How did you resolve the problem? > > Thanks again! > > From: jessebledsoe(a)gmail.com [mailto:jessebledsoe@gmail.com] On Behalf Of > Jesse Bledsoe > Sent: Wednesday, April 27, 2011 1:19 PM > To: Gallen, Courtney (NIH/NIDA) [F]; Freesurfer Mailing List > Subject: Re: [Freesurfer] Interpreting results from Qdec > > Hi Courtney, > > I'm no expert but I recalled a post similar to yours awhile ago with the > same question you ask. Doug and Nick offered an answer that may be of > help: > > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15586.html > > Jesse > On Wed, Apr 27, 2011 at 1:12 PM, Gallen, Courtney (NIH/NIDA) [F] > <gallencl(a)nida.nih.gov<mailto:gallencl@nida.nih.gov>> wrote: > Hi Doug > > Have a follow up question regarding significance levels in Qdec related to > extracting means from ROIs, etc. I'm posting to the entire mailing list in > case anyone else has ideas. > > Basically, I extracted mean volumes (from my set of participants) of ROIs > for which Qdec reports an interaction between two variables. I want to > look at these mean volumes in something like SPSS to see what is driving > the interaction/generate figures, etc. > > I'm having an issue with one such ROI, in that when I extract the mean > volumes and look for this interaction in SPSS, it is not significant (p ~ > 0.5, so really not significant at all). Is there any way that an ROI could > be significant in Qdec (p of 0.05, Monte Carlo sim), but not in SPSS when > I extract means for each participant? > > Let me know if this isn't clear. Any thoughts would be appreciated! > Courtney > > > Courtney Gallen > Post-baccalaureate IRTA > Neuroimaging Research Branch > National Institute on Drug Abuse (IRP) > 251 Bayview Blvd > Suite 200 > Baltimore, MD 21224 > Tel: (443) 740-2631<tel:%28443%29%20740-2631> > > -----Original Message----- > From: Douglas Greve > [mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>] > Sent: Tuesday, April 26, 2011 1:06 PM > To: Gallen, Courtney (NIH/NIDA) [F] > Subject: Re: [Freesurfer] Interpreting results from Qdec > > Those are the values outside (first column) and inside (2nd col) the > ROI. You can add "--id 1" to only report the values inside the ROI. > > doug > > On 4/26/11 1:02 PM, Gallen, Courtney (NIH/NIDA) [F] wrote: >> It worked! >> Now, last question. The txt file has two separate values (?averages). >> What do they each represent? >> >> -----Original Message----- >> From: Douglas Greve >> [mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>] >> Sent: Tuesday, April 26, 2011 12:53 PM >> To: Gallen, Courtney (NIH/NIDA) [F] >> Subject: Re: [Freesurfer] Interpreting results from Qdec >> >> try "--slabel fsaverage lh ROI-drawn-on-QDEC-brain.label" >> >> >> On 4/26/11 12:52 PM, Gallen, Courtney (NIH/NIDA) [F] wrote: >>> Actually, I hope I'm wrong about what I thought below. If I specify >>> individual subject's label and run: >>> >>> mri_segstats --in >>> /prot/Mprot/CTQ/freesurferDone/8579/surf/lh.volume.fwhm10.fsaverage.mgh >>> --slabel 8579 lh >>> /prot/Mprot/CTQ/freesurferDone/8579/label/lh.SupTemp_CTQxBDNFctrls.label >>> --avgwf lhSupTempctrls.txt >>> >>> I still get the same error about dimension mismatch >>> >>> >>> -----Original Message----- >>> From: Gallen, Courtney (NIH/NIDA) [F] >>> Sent: Tuesday, April 26, 2011 12:43 PM >>> To: 'Douglas Greve' >>> Subject: RE: [Freesurfer] Interpreting results from Qdec >>> >>> Ah I think I see the problem now. >>> >>> The label I originally specified is the general label created from the >>> ROI drawing in Qdec. Instead, I should use the individual subject's >>> label (from 'Map Label to Subjects') instead, right? >>> >>> Thank you! >>> >>> -----Original Message----- >>> From: Douglas Greve >>> [mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>] >>> Sent: Tuesday, April 26, 2011 12:38 PM >>> To: Gallen, Courtney (NIH/NIDA) [F] >>> Subject: Re: [Freesurfer] Interpreting results from Qdec >>> >>> You have to use the subject that matches the input, fsaverage in this >>> case. How did you define your label? If you defined it on subject 123, >>> you can transfer it to fsaverage using mri_label2label. >>> doug >>> >>> On 4/26/11 12:28 PM, Gallen, Courtney (NIH/NIDA) [F] wrote: >>>> Not a problem at all! >>>> >>>> If I use --in, I get an error saying that there is a dimension >>>> mismatch between input volume and seg. >>>> >>>> Any other thoughts? Thanks again! >>>> >>>> -----Original Message----- >>>> From: Douglas Greve >>>> [mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>] >>>> Sent: Tuesday, April 26, 2011 11:40 AM >>>> To: Gallen, Courtney (NIH/NIDA) [F] >>>> Subject: Re: [Freesurfer] Interpreting results from Qdec >>>> >>>> >>>> Hi Courtney, sorry for the delay. If more than a few days go by >>>> without >>>> a response, feel free to repost -- I promise not to get annoyed! >>>> Sometimes, things get pushed up and out of my mail browser window, and >>>> I >>>> often don't get back to them. Sorry! >>>> >>>> To answer your question, try using --in where you have --seg. The >>>> "segmentation" is actually already specified because you've specified >>>> a >>>> label. >>>> >>>> doug >>>> >>>> On 4/26/11 11:03 AM, Gallen, Courtney (NIH/NIDA) [F] wrote: >>>>> Hi Doug, >>>>> Sorry to keep bugging you but any thoughts about my response to your >>>>> e-mail from 2 weeks ago? I've given the exact command line I'm using >>>>> with mri_segstats. >>>>> Thanks again for all your help >>>>> Courtney >>>>> >>>>> -----Original Message----- >>>>> From: Gallen, Courtney (NIH/NIDA) [F] >>>>> Sent: Tuesday, April 12, 2011 10:59 AM >>>>> To: 'Douglas N Greve' >>>>> Subject: RE: [Freesurfer] Interpreting results from Qdec >>>>> >>>>> That may be the problem. ${sub} is an actual person's directory >>>>> >>>>> E.g., sub# 123--command line would be: >>>>> mri_segstats --seg >>>>> /prot/Mprot/CTQ/freesurferDone/123/surf/lh.volume.fwhm10.fsaverage.mgh >>>>> --slabel 123 lh \ >>>>> lh.SupTemp_CTQxBDNFctrls.label --avgwf lhSupTempctrls.txt >>>>> >>>>> >>>>> >>>>> -----Original Message----- >>>>> From: Douglas N Greve >>>>> [mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>] >>>>> Sent: Tuesday, April 12, 2011 10:55 AM >>>>> To: Gallen, Courtney (NIH/NIDA) [F] >>>>> Subject: Re: [Freesurfer] Interpreting results from Qdec >>>>> >>>>> What is your full command-line? Without variables, just something >>>>> that >>>>> you could put directly into the terminal. Make sure that you are >>>>> specifying fsaverage as your subject (can't tell below because your >>>>> use >>>>> ${sub}). >>>>> >>>>> doug >>>>> >>>>> >>>>> Gallen, Courtney (NIH/NIDA) [F] wrote: >>>>>> Sorry, but I can't seem to figure out how to specify input data. I >>>>>> tried '--in' but get an error that the input vol and seg label are >>>>>> not the same dimensions. I've been looking at the help options for >>>>>> mri_segstats (http://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats) >>>>>> but don't see it >>>>>> >>>>>> -----Original Message----- >>>>>> From: Douglas N Greve >>>>>> [mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>] >>>>>> Sent: Friday, April 08, 2011 10:38 AM >>>>>> To: Gallen, Courtney (NIH/NIDA) [F] >>>>>> Subject: Re: [Freesurfer] Interpreting results from Qdec >>>>>> >>>>>> The lh.volume.fwhm10.fsaverage.mgh should be your input. It is not >>>>>> a >>>>>> segmentation. You've already specified the seg with the the --slabel >>>>>> command. >>>>>> doug >>>>>> >>>>>> >>>>>> Gallen, Courtney (NIH/NIDA) [F] wrote: >>>>>> >>>>>>> One last question (hopefully). I'm specifying the input volume with >>>>>>> --seg, but am getting an error ('cannot do frame average without >>>>>>> input volume'). Am I missing something obvious? >>>>>>> >>>>>>> The entire command looks something like this: >>>>>>> mri_segstats --seg >>>>>>> /prot/Mprot/CTQ/freesurferDone/${sub}/surf/lh.volume.fwhm10.fsaverage.mgh >>>>>>> --slabel ${sub} lh \ >>>>>>> lh.SupTemp_CTQxBDNFctrls.label --avgwf lhSupTempctrls.txt >>>>>>> >>>>>>> Thanks again >>>>>>> -----Original Message----- >>>>>>> From: Douglas N Greve >>>>>>> [mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>] >>>>>>> Sent: Tuesday, April 05, 2011 4:21 PM >>>>>>> To: Gallen, Courtney (NIH/NIDA) [F] >>>>>>> Cc: Nick Schmansky; Freesurfer Mailing List >>>>>>> Subject: Re: [Freesurfer] Interpreting results from Qdec >>>>>>> >>>>>>> yes, something like ?h.volume.fwhm10.fsaverage.mgh >>>>>>> doug >>>>>>> >>>>>>> Gallen, Courtney (NIH/NIDA) [F] wrote: >>>>>>> >>>>>>> >>>>>>>> Hi Doug >>>>>>>> >>>>>>>> Thanks for helping me with this! >>>>>>>> >>>>>>>> First time around I did everything as is outlined in 'Define a >>>>>>>> Region of Interest' here: >>>>>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis. >>>>>>>> >>>>>>>> I'll try your suggestion now. The input data would be something >>>>>>>> like ?h.volume.fwhm10.fsaverage.mgh, correct? >>>>>>>> >>>>>>>> Thanks again >>>>>>>> Courtney >>>>>>>> >>>>>>>> -----Original Message----- >>>>>>>> From: Douglas N Greve >>>>>>>> [mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>] >>>>>>>> Sent: Thursday, March 31, 2011 5:44 PM >>>>>>>> To: Gallen, Courtney (NIH/NIDA) [F] >>>>>>>> Cc: Nick Schmansky; Freesurfer Mailing List >>>>>>>> Subject: Re: [Freesurfer] Interpreting results from Qdec >>>>>>>> >>>>>>>> Hi Courtney, did you transfer the label to each individual subject >>>>>>>> using >>>>>>>> mri_label2label? A better way to replicate your qdec results is to >>>>>>>> run >>>>>>>> mri_segstats on the input data to qdec (y.mgh usually). Specify >>>>>>>> the >>>>>>>> label with "--slabel subject hemi yourlabel". Also specify >>>>>>>> "--avgwf >>>>>>>> subjectdata.txt". This will create this text file with a list of >>>>>>>> the >>>>>>>> input data for each subject averaged over your label. >>>>>>>> >>>>>>>> doug >>>>>>>> >>>>>>>> Gallen, Courtney (NIH/NIDA) [F] wrote: >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>> Hi Nick >>>>>>>>> >>>>>>>>> I'm revisiting this issue and have a few more questions. First, I >>>>>>>>> have a significant interaction between two variables on cortical >>>>>>>>> volume. I drew a label on this ROI and ran mris_anatomical_stats >>>>>>>>> on the label (thank you for that suggestion). >>>>>>>>> >>>>>>>>> For stats in the output table file, is the column 'GrayVol' the >>>>>>>>> same thing as the cortical volume I looked at in Qdec? I'm asking >>>>>>>>> because when I export GrayVol values into SPSS, there is no >>>>>>>>> longer a significant interaction between my variables (and if >>>>>>>>> this ROI is significant after multiple comparisons across the >>>>>>>>> brain, I'd expect the mean volume from the ROI to be very >>>>>>>>> significant in SPSS). >>>>>>>>> >>>>>>>>> Please let me know if my questions aren't clear. Thanks in >>>>>>>>> advance >>>>>>>>> Courtney >>>>>>>>> >>>>>>>>> >>>>>>>>> Courtney Gallen >>>>>>>>> Post-baccalaureate IRTA >>>>>>>>> Neuroimaging Research Branch >>>>>>>>> National Institute on Drug Abuse (IRP) >>>>>>>>> 251 Bayview Blvd >>>>>>>>> Suite 200 >>>>>>>>> Baltimore, MD 21224 >>>>>>>>> Tel: (443) 740-2631<tel:%28443%29%20740-2631> >>>>>>>>> >>>>>>>>> >>>>>>>>> -----Original Message----- >>>>>>>>> From: Nick Schmansky >>>>>>>>> [mailto:nicks@nmr.mgh.harvard.edu<mailto:nicks@nmr.mgh.harvard.edu>] >>>>>>>>> Sent: Thursday, January 13, 2011 3:08 PM >>>>>>>>> To: Gallen, Courtney (NIH/NIDA) [F] >>>>>>>>> Cc: Freesurfer Mailing List >>>>>>>>> Subject: Re: [Freesurfer] Interpreting results from Qdec >>>>>>>>> >>>>>>>>> Courtney, >>>>>>>>> >>>>>>>>> if i understand your question, i think one way to do that is to >>>>>>>>> use qdec >>>>>>>>> to draw a label on the blob of interest, and the run 'map label >>>>>>>>> to >>>>>>>>> subjects', which creates a label file in each subjects label dir, >>>>>>>>> then >>>>>>>>> you can run stats on that with mris_anatomical_stats. >>>>>>>>> >>>>>>>>> (btw, i'm putting this answer on the list, as others may have >>>>>>>>> better >>>>>>>>> ideas.) >>>>>>>>> >>>>>>>>> n. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> On Mon, 2011-01-03 at 16:38 -0500, Gallen, Courtney (NIH/NIDA) >>>>>>>>> [F] >>>>>>>>> wrote: >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>>> Hi Nick >>>>>>>>>> >>>>>>>>>> Thanks for the prompt reply. Sorry if my questions seem a bit >>>>>>>>>> naïve--this is my first time using Freesurfer. >>>>>>>>>> >>>>>>>>>> A follow up question to your answer for question 1. I see that >>>>>>>>>> the group data will be plotted in Qdec for significant blobs, >>>>>>>>>> but say there is a significant interaction between two variables >>>>>>>>>> and it's not entirely apparent what is driving this interaction. >>>>>>>>>> Is there a way to extract the mean of this blob for each >>>>>>>>>> individual (i.e., treat it as an ROI or something similar) to >>>>>>>>>> determine what's driving the significance? >>>>>>>>>> >>>>>>>>>> Thanks in advance! >>>>>>>>>> Courtney >>>>>>>>>> >>>>>>>>>> -----Original Message----- >>>>>>>>>> From: Nick Schmansky >>>>>>>>>> [mailto:nicks@nmr.mgh.harvard.edu<mailto:nicks@nmr.mgh.harvard.edu>] >>>>>>>>>> Sent: Thursday, December 30, 2010 2:44 PM >>>>>>>>>> To: Gallen, Courtney (NIH/NIDA) [F] >>>>>>>>>> Cc: >>>>>>>>>> freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> >>>>>>>>>> Subject: Re: [Freesurfer] Interpreting results from Qdec >>>>>>>>>> >>>>>>>>>> ans. 1. - the easiest way is to Ctrl- left mouse click on a >>>>>>>>>> blob, and a >>>>>>>>>> plot of the data at that surface vertex will appear. the group >>>>>>>>>> will be >>>>>>>>>> apparent from that (say, demented group is thinner than >>>>>>>>>> non-demented >>>>>>>>>> group). this data is significance data (log p, so '2' is 0.01), >>>>>>>>>> so mean >>>>>>>>>> and stdev wouldnt apply in that case. the file 'y.mgh' is the >>>>>>>>>> raw data >>>>>>>>>> of all subjects in the analysis, so you could extract mean and >>>>>>>>>> stdev >>>>>>>>>> from that. >>>>>>>>>> >>>>>>>>>> ans. 2. - slide the 'annotation' opacity slider to show the >>>>>>>>>> annotation >>>>>>>>>> data (cortical parcellation). the ctrl left click will also put >>>>>>>>>> the >>>>>>>>>> region info for that vertex on the lower left of the display. >>>>>>>>>> >>>>>>>>>> see also: >>>>>>>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis >>>>>>>>>> >>>>>>>>>> n. >>>>>>>>>> >>>>>>>>>> On Wed, 2010-12-29 at 10:49 -0500, Gallen, Courtney (NIH/NIDA) >>>>>>>>>> [F] >>>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>>> Hi, >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> I'm currently running analyses in Qdec and have identified >>>>>>>>>>> areas that >>>>>>>>>>> show significant effects in my contrasts. I have two questions >>>>>>>>>>> related >>>>>>>>>>> to interpreting these results. >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> 1. How can you interpret the effect in each "blob?" (i.e., >>>>>>>>>>> which >>>>>>>>>>> group has a greater cortical surface area, etc.). Right now, >>>>>>>>>>> all I >>>>>>>>>>> know is that there is an effect in certain areas. Can you >>>>>>>>>>> export this >>>>>>>>>>> data to get means and standard errors? >>>>>>>>>>> >>>>>>>>>>> 2. Is there a way to localize where these effects are? >>>>>>>>>>> E.g., a >>>>>>>>>>> tool that tells you this effect is located in __ area of the >>>>>>>>>>> brain? >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Thanks in advance >>>>>>>>>>> >>>>>>>>>>> Courtney >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Courtney Gallen >>>>>>>>>>> >>>>>>>>>>> Post-baccalaureate IRTA >>>>>>>>>>> >>>>>>>>>>> Neuroimaging Research Branch >>>>>>>>>>> >>>>>>>>>>> National Institute on Drug Abuse (IRP) >>>>>>>>>>> >>>>>>>>>>> 251 Bayview Blvd >>>>>>>>>>> >>>>>>>>>>> Suite 200 >>>>>>>>>>> >>>>>>>>>>> Baltimore, MD 21224 >>>>>>>>>>> >>>>>>>>>>> Tel: (443) 740-2631<tel:%28443%29%20740-2631> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> Freesurfer mailing list >>>>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> The information in this e-mail is intended only for the person >>>>>>>>>> to whom it is >>>>>>>>>> addressed. If you believe this e-mail was sent to you in error >>>>>>>>>> and the e-mail >>>>>>>>>> contains patient information, please contact the Partners >>>>>>>>>> Compliance HelpLine at >>>>>>>>>> http://www.partners.org/complianceline . If the e-mail was sent >>>>>>>>>> to you in error >>>>>>>>>> but does not contain patient information, please contact the >>>>>>>>>> sender and properly >>>>>>>>>> dispose of the e-mail. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Freesurfer mailing list >>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Freesurfer mailing list >>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > Jesse C. Bledsoe, M.A. > Ph.D. Candidate, Clinical Psychology > Consortium for Neurodevelopmental Study > Department of Psychology > 110E Psychology Building > Michigan State University > East Lansing, MI 48824 > ______________________________________ > > Note: Information contained in this electronic message and any attachments > to this message are intended for the exclusive use of the addressee(s) and > may contain proprietary, confidential or privileged information. If you > are > not the intended recipient, you should not disseminate, distribute or copy > this e-mail. Please notify the sender immediately and destroy all copies > of > this message and any attachments. > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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