Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30089 discussions

Re: [Freesurfer] Differences between BrainSuite and FreeSurfer
by Patterson, James 11 Sep '12

11 Sep '12

Sorry about that, mailing list cc’d. Reply vs reply all… Stuff attached, but also uploaded. (message bounced) The colorscale.tiff is an example of the strange color scale abnormality, and the colorscaleabnormality.png shows the settings to get a similar one. The PPTX shows the results – better. The vertex-for-examination.png shows a vertex location that I have questions about – in the BrainSuite image this vertex is apparently normal, and in FreeSurfer results it’s low. With regards to the original question: – still some abnormalities, but the head-coil difference appeared to have played a large role in the lack of signal in the group comparison. Thanks, JP --- James C. Patterson II, MD, PhD Professor of Psychiatry LSU Health - Shreveport --- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tuesday, September 11, 2012 6:22 AM To: Patterson, James Subject: Re: [Freesurfer] Differences between BrainSuite and FreeSurfer Good. Send a tif with your threshold and max (and cc the list) On Sep 11, 2012, at 6:58 AM, "Patterson, James" <JPatte(a)lsuhsc.edu<mailto:JPatte@lsuhsc.edu>> wrote: It was the head coil! There are still some differences, but I need to control variables better before I come to you with that. One last thing: Can you tell me why the color scales are strange looking when I choose Blue-red? This isn’t the complex setting….am I missing a library file or something? Running Mac OSX latest version --- James C. Patterson II, MD, PhD Professor of Psychiatry LSU Health - Shreveport --- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, September 10, 2012 8:22 PM To: Patterson, James Subject: Re: [Freesurfer] Differences between BrainSuite and FreeSurfer Hi James Just click on it in tksurfer and it will show the vertex number Bruce On Sep 10, 2012, at 2:11 PM, "Patterson, James" <JPatte(a)lsuhsc.edu<mailto:JPatte@lsuhsc.edu>> wrote: <image001.jpg> <image002.png>Bruce, I’m not sure how to get a vertex location out, but left hemisphere, and in the area circled. --- James C. Patterson II, MD, PhD Professor of Psychiatry LSU Health - Shreveport --- -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, September 10, 2012 8:32 AM To: Patterson, James Subject: Re: [Freesurfer] Differences between BrainSuite and FreeSurfer Hi James can you give me a vertex location and hemisphere where you expect to see an effect in FS, but don't? thanks Bruce On Sat, 8 Sep 2012, Patterson, James wrote: > Hello, > > I'm trying to figure out why I am getting differences in apparent cortical thickness between BrainSuite11a and Freesurfer. > > I have a patient scan - high res SPGR BRAVO off a GE 1.5T scanner. > > In BrainSuite, their are marked decreases in cortical thickness that is consistent with the patients TBI. > > In FreeSurfer, the changes are quite bit more subtle, and when I compare this one image to a group of normal images (the feature that is very attractive about freesurfer), I do not get anything close to what I would expect. > > Is there a way to post images? Or perhaps links to images on another site? > > I am not sure where to begin to search for answers as to why I am getting these differences. > > I would be happy to answer more questions - I likely have not provided enough information. > > James Patterson > _______________________________________________ > 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. <colorscale.tiff>

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Repost: Converting BV ROIs to FS
by Katie Bettencourt 11 Sep '12

11 Sep '12

> So our lab is running a couple analyses and we are getting different > results based on whether we use Brain Voyager or Freesurfer that we think > is due to different ROI selection across the two platforms. Is there > anyway to load a BrainVoyager ROI into freesurfer? The BV data has been > talairach transformed, does that matter? Less optimal would be loading a > freesurfer ROI into BV, but if that's easier, we could try that way too. > > Any help would be appreciated. > > Katie >

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surface does match - how to verify subjects
by Darren Gitelman 11 Sep '12

11 Sep '12

Hi I was trying to create an average subject using the make_average_subject command. When it got to one of the subjects there was the following error: #@# processing subject 4/85 3106... Reading /home/drg/3106/surf/lh.sphere.reg mrisReadTriangleFile(/home/drg/3106/surf/lh.orig): surface doesn't match /home/drg/3106/surf/lh.sphere.reg No such file or directory mrisReadTriangleFile failed. No such file or directory MRISreadOriginalProperties: could not read surface file orig No such file or directory mris_make_average_surface: could not read orig file for lh. No such file or directory mris_average_surface failed ERROR: make_average_surface --------- Looking in the surf directory both lh.orig and lh.surf.reg exist, but I'm guessing this means I need to run the recon-all -s <subjid> -make all command. My question is whether there is some command I can use to validate subjects before trying to run commands such as make_average_subject. I want to avoid the situation where I fix this subject, then try to rerun make_average_subject only to find that some other subject also needs fixing. Thanks, -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073

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Re: [Freesurfer] problem with tksurfer
by Douglas N Greve 11 Sep '12

11 Sep '12

Hi Maryam, I finally figured out what is going on. The bottom line is that it is just a weird coincidence. The volume size is 70*70*33=161700 which happens to be exactly how many vertices are in the left hemisphere of this subject. When tksurfer sees this, it thinks that each voxel must be a vertex and displays it as such instead of sampling the volume onto surface which is why it looks so strange. There is not a way to force tksurfer to treat the overlay as a volume, but instead (and probably better), you can sample the volume onto the surface, then load it as an overlay, eg mri_vol2surf --reg register.dof6.dat --hemi lh --mov sig.nii.gz --o lh.sig.mgh --projfrac 0.5 tksurfer teal_tiger_kcb lh inflated -curv -overlay lh.sig.mgh and the same thing with the right side. The chances that this kind of thing happens must be several million to one! doug On 09/06/2012 05:26 PM, Maryam Vaziri Pashkam wrote: > Hi Doug, > > I uploaded the tar file. It is called incorrect_lh_test.tar > > Thanks, > Maryam > > On Wed, Sep 5, 2012 at 10:04 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Can you upload a tarball of the subject and the sig.nii.gz to our > file drop? > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > doug > > > > On 08/28/2012 10:18 AM, Maryam Vaziri Pashkam wrote: > > Hi Doug, > > Any other insight how I can solve this problem? > > Maryam > > On Fri, Aug 24, 2012 at 7:17 PM, Maryam Vaziri Pashkam > <mvaziri(a)fas.harvard.edu <mailto:mvaziri@fas.harvard.edu> > <mailto:mvaziri@fas.harvard.edu > <mailto:mvaziri@fas.harvard.edu>>> wrote: > > It looks fine to me. I have attached the tiff image of a > coronal > slice. So this means that the registration of the surface > to the > anatomical is fine. This is strange. I tried the tksurfer > with the > original surface and the overlay on the rh looks fine and > the left > hemisphere has the same problem as on the inflated > surface. Any > other idea? > > M > > > On Fri, Aug 24, 2012 at 6:54 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > > I don't understand your last paragraph. Does the lh > surface > look ok, eg, when you run > > tkmedit teal_tiger_kcb orig.mgz -surfs > > doug > > > > > On 08/24/2012 06:37 PM, Maryam Vaziri Pashkam wrote: > > Yes I have checked it multiple times. They are the > same. > Here are the two lines: > > tksurfer teal_tiger_kcb rh inflated -curv -overlay > > /Users/maryam/mri-space/studies/SM_PDM_2cat/unpackdata/120421_xu_SM2CAT_06/bold/Cat_all/taskvsfix/sig.nii.gz > -overlay-reg > > /Users/maryam/mri-space/studies/SM_PDM_2cat/unpackdata/120421_xu_SM2CAT_06/bold/register.dof6.dat > -scalebarflag 1 > > tksurfer teal_tiger_kcb lh inflated -curv -overlay > > /Users/maryam/mri-space/studies/SM_PDM_2cat/unpackdata/120421_xu_SM2CAT_06/bold/Cat_all/taskvsfix/sig.nii.gz > -overlay-reg > > /Users/maryam/mri-space/studies/SM_PDM_2cat/unpackdata/120421_xu_SM2CAT_06/bold/register.dof6.dat > -scalebarflag 1 > > I have copy pasted the inflated anatomical folder > of the > subject from another computer. Is it possible that > some > specific files are not copied properly? I dont > know where > are the files that have the information for > registration > of the anatomical brain to the inflated suface. My > guess > is that is where the problem is. What do you think? > > > Maryam > > > > On Fri, Aug 24, 2012 at 6:19 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > Hi Maryam, it seems very strange that one > hemisphere > looks ok but > other looks bad. In fact, I'd say that it cannot > happen. The > differences are not likely to be due to > version. Can > you double > check that the tksurfer commands for the lh > and rh are > the same > (except for lh and rh, of course) > doug > > > > > On 08/22/2012 09:13 PM, Maryam Vaziri Pashkam > wrote: > > Hi Doug, > > I am having a problem with tksurfer overlay > function. I ran > one analysis in freesurfer 5.1 on a mac > machine > and I cannot > properly load it on the surface. The > analysis was > performed in > the native space. When I use tksurfer to > load the > analysis on > the surface using the overlay function I > dont get > an error but > the output image just shows small dots on the > surface instead > of patches of activity. It looks like the > registration is not > correct. I checked the registration on the > volume > and it looks > fine to me. This only happens with one of my > subject and only > on his left hemisphere. I have attached > two tif > images called > lhnative.tif and rhnative.tif that show the > results. I also > ran the analysis on the surface for both > left and > right > hemisphere, and it looks fine (lhsurf.tif and > rhsurf.tif files > attached). > Any Idea how to solve this problem? My > guess is > that the error > is in the registration of anatomical volume to > anatomical > surface in the left hemisphere of this > specific > subject, but I > dont know how to solve this issue. > > here is the code that I use to load the > data on > the surface: > > tksurfer teal_tiger_kcb lh inflated -curv > -overlay > > /Users/maryam/mri-space/studies/SM_PDM_2cat/unpackdata/120421_xu_SM2CAT_06/bold/Cat_all/taskvsfix/sig.nii.gz > -overlay-reg > > /Users/maryam/mri-space/studies/SM_PDM_2cat/unpackdata/120421_xu_SM2CAT_06/bold/register.dof6.dat > -scalebarflag 1 > > Just a note that the recon-all was > performed in > freesurfer 4.5 > and the analysis on freesurfer 5.1. Any chance > this might have > caused the error? > > Thanks, > Maryam > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 > <tel:617-726-7422> > > <tel:617-726-7422 <tel: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> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > The information in this e-mail is intended > only for > the person to > whom it is > addressed. If you believe this e-mail was sent > to you > in error and > the e-mail > contains patient information, please contact > the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was > sent to > you in error > but does not contain patient information, please > contact the > sender and properly > dispose of the e-mail. > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel: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> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Coordinate transformation between raw space and freesurfer confirm space
by liang wang 11 Sep '12

11 Sep '12

Hi, I need to convert a vast amount of coordinates (voxel unit: i, j, k) in raw space to freesurfer space (256*256*256 FOV). Could someone give some suggestions how to solve it? Thanks, Liang

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qdec analyses without interaction effect
by Shannon Kogachi 10 Sep '12

10 Sep '12

Hi, I was wondering if there is a way to run statistical tests, such as a 2-way ANCOVA, on QDEC but without the interaction effect. I ran a 2-way ANCOVA for thickness measures for a longitudinal study, and no interaction effect was found. Therefore, I would like to run the same test but without the interaction effect and see if there are other group effects. Please let me know if there is a way to do this in QDEC or any other statistical programs in FreeSurfer. Thank you! -Shannon

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Questions on QA Tools
by Irwin, William 10 Sep '12

10 Sep '12

Hi- This is an useful addition. I have a couple of questions about the outputs: 1. "<subject> has 36 outliers": I assume this refers to the volumetrics as compared to FS Average, where an outlier is a volume +/- 2 SDs? 2. "7927 vertices did not have an annotation!:" I understand what this means, but what are the QA implications? Thanks, Wil

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qdec.table.dat file
by Fidel Vila 10 Sep '12

10 Sep '12

Hi Freesurfer experts, A newbie question regarding working with QDEC. When I try to upload the qdec.table.dat file (attached) an error messages pops up "Error loading the data table". To the best of my knowledge I've followed the guidelines on the tutorial in terms of formatting. What would be your suggestions to troubleshoot this? Thanks! Fidel

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mri_vol2surf problem
by Garikoitz Lerma Usabiaga 10 Sep '12

10 Sep '12

Dear freesurfers, I am trying to create .mgh labels in order to obtain CT averages from several subjects. I register the ROI-s with bbregister and I get the .nii which renders nicely in tksurfer: tksurfer Surfrend_Colin127 lh inflated -overlay /Applications/freesurfer/subjects/ROI10/BrocaOrb_2mm.nii -overlay-reg /Applications/freesurfer/subjects/ROI10/bbregister_singlesubject_to_Colin.dat -fthresh 1 The problem arises when I try to use mri_vol2surf. I've been trying with many different options, for example: mri_vol2surf --mov /Applications/freesurfer/subjects/ROI10/BrocaOrb_2mm.nii --reg /Applications/freesurfer/subjects/ROI10/bbregister_singlesubject_to_Colin.dat --projfrac 0.5 --projfrac-max 0 1 .01 --hemi lh --out /Applications/freesurfer/subjects/ROI10/lh.BA44-45-47.mgh or mri_vol2surf --mov /Applications/freesurfer/subjects/ROI10/BrocaOrb_2mm.nii --reg /Applications/freesurfer/subjects/ROI10/bbregister_singlesubject_to_Colin.dat --projdist-max 0 1 0.1 --projfrac 1 --interp nearest --hemi lh --out /Applications/freesurfer/subjects/ROI10/lh.BA44-45-47.mgh When I try to visualize it with tksurfer, it gives me nothing: tksurfer Surfrend_Colin27 lh inflated -label /Applications/freesurfer/subjects/ROI10/lh.BA44-45-47.mgh -fthresh 1 How should I use mri_vol2surf in order to obtain results? What are the alternatives in order to have surface labels? Creating a label tracing the border of the .nii label in tksurfer is a posible solution? Thank you very much for your attention, Gari [iMacGari:~] garikoitz% mri_vol2surf --mov /Applications/freesurfer/subjects/ROI10/BrocaOrb_2mm.nii --reg /Applications/freesurfer/subjects/ROI10/bbregister_singlesubject_to_Colin.dat --projfrac 0.5 --projfrac-max 0 1 .01 --hemi lh --out /Applications/freesurfer/subjects/ROI10/lh.BA44-45-47.mgh srcvol = /Applications/freesurfer/subjects/ROI10/BrocaOrb_2mm.nii srcreg = /Applications/freesurfer/subjects/ROI10/bbregister_singlesubject_to_Colin.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 1 INFO: float2int code = 0 Done loading volume Reading surface /Applications/freesurfer/subjects/Surfrend_Colin127/surf/lh.white Done reading source surface Reading thickness /Applications/freesurfer/subjects/Surfrend_Colin127/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0 0 1 using old 2 0.01 0 1 using old 3 0.02 0 1 [...] 99 0.979999 0 1 using old 100 0.989999 0 1 using old 101 0.999999 0 1 using old Done mapping volume to surface Number of source voxels hit = 32875 Writing to /Applications/freesurfer/subjects/ROI10/lh.BA44-45-47.mgh Dim: 165607 1 1

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Running @SUMA_Make_Spec_FS after FreeSurfer.
by Hye Young Heo 10 Sep '12

10 Sep '12

Hello, I successfully finished making the cortical surface using the " recon-all " command. For functional analysis, I tried to used the AFNI and SUMA. To create the spec files and AFNI files, I used the @SUMA_Make_Spec_FS. but I got the error. Warning: Found COR files and mri/orig.mgz ******** Will use COR files. echo: No match. grep: COR-.info: No such file or directory grep: COR-.info: No such file or directory grep: COR-.info: No such file or directory set: No match. I think the SUMA script tried to used the COR files to create AFNI file or convert COR file if there is a *.mgz file. After Freesurfer, I found the mgz file, but no COR files in the freesurfer directory. Thanks.

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