Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30065 discussions

Using .label file as mask in mri_fdr
by Chen Jen-I. 14 Mar '18

14 Mar '18

Hello, I want to do a FDR correction using mri_fdr within a ROI mask (in .label format). I see the option of passing the sig.mgh volume through a mask, and I read that one can use the mask.mgh in the GLMFIT folder. What is this mask.mgh? I tried to visualize it in Freeview but it doesn’t look like a mask but rather some sort of geometric form. If I have labels as my ROI, how do I convert that into a .mgh format to be used in mri_fdr? (I tried simply using the label file first and obviously that didn’t work…) Thank you in advance, Jeni Chen

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Report Effect Sizes of Significant Clusters - using .mgh files
by Hannah Claussenius-Kalman 14 Mar '18

14 Mar '18

We used the gamma.mgh and rstd.mgh files to derive an effect size file that we called cohensd.mgh. How can I access these files to report effect size (Cohen's *d*) for significant clusters?

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(no subject)
by Sudeshna 14 Mar '18

14 Mar '18

Hello Freesurfer experts, While doing manual edits, I have had a problem editing the pial surface. When I look at the coronal view of the temporal lobe, the pial boundary does not track properly but the white matter boundary is fine. I have had circumstances where both the pial and white matter boundaries have problems and have been able to correct the issue by editing the white matter. However, in this instance, I am not sure how to fix the problem. Could somebody please tell me how to alter the pial boundary when the white matter boundary is correct? My second issue is a ‘tagging’ issue. While the boundary is correctly drawn, there are little red specks. I am not sure if this is a problem and if so, what I should do to fix it. Thanks in advance, Sudeshna P.S. I have attached some screenshots of the problem described above.

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Get center coordinates of ROIs from the Lausanne2008 parcellation
by Laura Juan Galmes 14 Mar '18

14 Mar '18

Hi all, I have a question about how to get a .nii or .mgz file out of a .gcs. What I actually want to do is get the coordinates of the centroids of the regions of my atlas ( which is lausanne2008), or even the coordinates of all the voxels in each region so I could compute the mean myself. However, I only have the gcs files (myatlas_125_rh.gcs and my atlas_125_lh.gcs) and have no idea on how to get this information. Thank you a lot in advance. Laura

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dt_recon error: MatrixReadTxT: could not scan value [1][1]
by Noriana Jakopin 13 Mar '18

13 Mar '18

Hello FreeSurfer Developers, I am trying to follow the diffusion processing pipeline describe in this tutorial: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/DiffusionV6.0#dMRIData… However, I keep getting an error when using dt_recon. For background, my input is 1700 dicom images. The code seems to run the Eddy/Motion Correct part. Once it reaches Fitting Tensors, I get the following messages: ---------------------- Creating output directory /mnt/c/Users/leonardo/Desktop/UMD/Linux-Windows/Hedyeh/MIDA_dtrecon Loading y from /mnt/c/Users/leonardo/Desktop/UMD/Linux-Windows/Hedyeh/MIDA_dtrecon/dwi-ec.nii.gz ... done reading. MatrixReadTxT: could not scan value [1][1] WARNING: matlab elment type is 1885959265, which is not a matrix. could not allocate 542270823 x 539828311 matrix Cannot allocate memory unsupported matlab format -1066407936 (unknown) Cannot allocate memory Permission denied -------------------- I saw a previous post with a similar error, however there was no answer to it: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg56652.html. My computer has almost 20 GB of free space, so there should be space for the resulting files to be created. Freesurfer version: freesurfer-Linux-centos6_x86-stable-pub-v6.0.0-2beb96c Platform: Linux (Ubuntu) subsystem for Window 10 Thank you, Noriana Jakopin

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Re: [Freesurfer] FSdev compilation error
by Hoopes, Andrew 13 Mar '18

13 Mar '18

Hi Victor, thanks, can you send the config.log for the original issue where configure fails and “--with-mni-dir=“ isn’t specified. best, Andrew On March 12, 2018 at 10:07:33 AM, Victor Hansen (victor.hansen(a)nru.dk<mailto:victor.hansen@nru.dk>) wrote: Hello Andrew Attached is our config.log I will try to build an older version too. Thank you -- Best regards Victor Hansen IT support Neurological Research Unit, Rigshospitalet nru.dk On Wed, 2018-03-07 at 17:45 +0000, Hoopes, Andrew wrote: Hi Victor, Can you send over the config.log? Also, it’s probably worth noting that the cuda dev builds are currently failing due to recent mrisurf.c changes (working on fixing this now), so if you’re trying to resolve this as soon as possible, it might make sense to checkout and build an older version. best Andrew On March 7, 2018 at 12:13:12 PM, Victor Hansen (victor.hansen(a)nru.dk<mailto:victor.hansen@nru.dk>) wrote: Hello Bruce I am the one inputting the commands - thanks for your tip about MNI libraries, I managed to point it towards the right location for them. However, the "make" step is now complaining about the PetSC libraries: https://paste.ubuntu.com/p/68G4sBB7DK/ I have tried to point it towards the local libraries with --with-petsc= but then ./configure complains that it can't find them at all. Thank you for your help. -- Best regards Victor Hansen IT support Neurological Research Unit, Rigshospitalet nru.dk On Wed, 2018-03-07 at 10:24 -0500, Bruce Fischl wrote: Hi Mel (and Victor?) the missing functions are all from the MNI lib. Not sure what you are missing. Maybe Andrew (ccd) knows? cheers Bruce On Wed, 7 Mar 2018, Melanie Ganz wrote: Dear list, In order to use a brandnew Nvidia GPU we downloaded FSdev and are trying to compile it locally with a new CUDA version. We get all the way to the configure command described on http://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page which is: ./configure --disable-Werror --with-cuda=/usr/local/cuda-9.1 --with-pkgs-dir=/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages --enable-fermi-gpu --libdir=/usr/lib64 Then there are no errors about any libraries, but instead errors about "undefined reference" in the files utils/mri.c and utils/mriio.c (see error below). I searched in the archives and couldn’t find anything about this. Any ideas? Cheers, Mel make[2]: Entering directory '/indirect/data2/Ganz/FSdev/freesurfer/mri_gdfglm' /bin/sh ../libtool --tag=CC --mode=link g++ -I../include -fdata-sections -ffunction-sections -Wl,--gc-sections -L/indirect/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/qt/current/lib -L/usr/lib64 -L/usr/X11R6/lib64 -fopenmp -fdata-sections -ffunction-sections -Wl,--gc-sections -Wl,-Map,ld_map.txt-Wl,--no-demangle -L/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/vxl/current/lib -L/data2/Ganz/FSdev/freesurfer/ce ntos6-x86_64-packages/itk/current/lib/InsightToolkit -o mri_gdfglm mri_gdfglm.o fsgdf.o ../utils/libutils.a ../fsgdf/libfsgdf.a ../rgb/librgb.a ../unix/libunix.a ../dicom/libdicom.a ../hipsstubs/libhipsstubs.a ../log/liblog.a ../xml2/libxml2.a ../jpeg/libjpeg.a ../tiff/libtiff.a ../expat/libexpat.a ../minc_1_5_1/libminc_1_5_1.a ../netcdf_3_6_0_p1/libnetcdf_3_6_0_p1.a/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKIO.a /data2/Ganz/FSdev/freesurfer/ centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKAlgorithms.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packa ges/itk/current/lib/InsightToolkit/libITKCommon.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insi ghtToolkit/libITKNumerics.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKMetaI O.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKniftiio.a /data2/Ganz/FSdev /freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKNrrdIO.a /data2/Ganz/FSdev/freesurfer/centos6-x86_ 64-packages/itk/current/lib/InsightToolkit/libitkpng.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib /InsightToolkit/libitksys.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitktiff. a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkv3p_netlib.a /data2/Ganz/FSde v/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkzlib.a /data2/Ganz/FSdev/freesurfer/centos6-x86_6 4-packages/itk/current/lib/InsightToolkit/libitkgdcm.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib /InsightToolkit/libitkopenjpeg.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitk jpeg8.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkjpeg12.a /data2/Ganz/FS dev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkjpeg16.a /data2/Ganz/FSdev/freesurfer/centos6-x 86_64-packages/itk/current/lib/InsightToolkit/libITKDICOMParser.a /usr/lib64/libuuid.so -lrt -lz -lm -lcrypt -ldl -lpthread -lvnl_algo -lvnl -lvcl -lnetlib -lv3p_netlib libtool: link: g++ -I../include -fdata-sections -ffunction-sections -Wl,--gc-sections -fopenmp -fdata-sections -ffunction-sections -Wl,--gc-sections -Wl,-Map -Wl,ld_map.txt -Wl,--no-demangle -o mri_gdfglm mri_gdfglm.o fsgdf.o /usr/lib64/libuuid.so -L/indirect/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/qt/current/lib -L/usr/lib64 -L/usr/X11R6/lib64 -L/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/vxl/current/lib -L/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit ../utils/libutils.a ../fsgdf/libfsgdf.a ../rgb/librgb.a ../unix/libunix.a ../dicom/libdicom.a ../hipsstubs/libhipsstubs.a ../log/liblog.a ../xml2/libxml2.a ../jpeg/libjpeg.a ../tiff/libtiff.a ../expat/libexpat.a ../minc_1_5_1/libminc_1_5_1.a ../netcdf_3_6_0_p1/libnetcdf_3_6_0_p1.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKIO.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKAlgorithms.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKCommon.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKNumerics.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKMetaIO.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKniftiio.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKNrrdIO.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkpng.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitksys.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitktiff.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkv3p_netlib.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkzlib.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkgdcm.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkopenjpeg.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkjpeg8.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkjpeg12.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkjpeg16.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKDICOMParser.a -lrt -lz -lm -lcrypt -ldl -lpthread -lvnl_algo -lvnl -lvcl -lnetlib -lv3p_netlib -fopenmp ../utils/libutils.a(mri.o): In function `MRIfree': /data2/Ganz/FSdev/freesurfer/utils/mri.c:5802: undefined reference to `delete_general_transform' ../utils/libutils.a(mri.o): In function `MRIcopyHeader': /data2/Ganz/FSdev/freesurfer/utils/mri.c:6069: undefined reference to `copy_general_transform' /data2/Ganz/FSdev/freesurfer/utils/mri.c:6072: undefined reference to `get_linear_transform_ptr' /data2/Ganz/FSdev/freesurfer/utils/mri.c:6073: undefined reference to `get_inverse_linear_transform_ptr' /data2/Ganz/FSdev/freesurfer/utils/mri.c:6067: undefined reference to `delete_general_transform' ../utils/libutils.a(mriio.o): In function `corRead': /data2/Ganz/FSdev/freesurfer/utils/mriio.c:1611: undefined reference to `input_transform_file' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:1612: undefined reference to `get_linear_transform_ptr' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:1613: undefined reference to `get_inverse_linear_transform_ptr' ../utils/libutils.a(mriio.o): In function `mincRead': /data2/Ganz/FSdev/freesurfer/utils/mriio.c:2316: undefined reference to `start_volume_input' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:2321: undefined reference to `get_volume_n_dimensions' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:2335: undefined reference to `get_volume_n_dimensions' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:2346: undefined reference to `get_volume_sizes' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:2355: undefined reference to `get_volume_nc_data_type' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:2386: undefined reference to `get_volume_separations' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:2425: undefined reference to `convert_voxel_to_world' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:2475: undefined reference to `get_voxel_to_world_transform' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:2476: undefined reference to `get_linear_transform_ptr' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:2456: undefined reference to `input_more_of_volume' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:2463: undefined reference to `get_volume_voxel_value' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:2485: undefined reference to `delete_volume_input' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:2486: undefined reference to `delete_volume' ../utils/libutils.a(mriio.o): In function `mghRead': /data2/Ganz/FSdev/freesurfer/utils/mriio.c:11472: undefined reference to `input_transform_file' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:11473: undefined reference to `get_linear_transform_ptr' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:11474: undefined reference to `get_inverse_linear_transform_ptr' collect2: error: ld returned 1 exit status Makefile:562: recipe for target 'mri_gdfglm' failed make[2]: *** [mri_gdfglm] Error 1 make[2]: Leaving directory '/indirect/data2/Ganz/FSdev/freesurfer/mri_gdfglm' Makefile:1048: recipe for target 'all-recursive' failed make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory '/indirect/data2/Ganz/FSdev/freesurfer' Makefile:957: recipe for target 'all' failed make: *** [all] Error 2 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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Negative areas in mris_sphere, dark in freeview
by Chris Adamson 13 Mar '18

13 Mar '18

Freesurfer devs, I have a baffling problem in mris_sphere. I have generated some surfaces using an external tool that uses VTK. After converting the surfaces into freesurfer format using a basic format converter, then adding volume geometry to the surface file using the image used to create it the surface appears dark in freeview. When I do mris_inflate followed by mris_sphere, mris_sphere says nearly all the triangles have negative area at the end and it never finishes. I verified in MATLAB that the surface normals (computed by mris_convert) of the original white surfaces point outwards. The darkness in freeview is not fixed by changing the order of the indices of the faces (which should invert the normal). I'm at a loss to explain this. Thanks in advance, Chris. Dr Chris Adamson Senior Research Officer Developmental Imaging, Clinical Sciences Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Road, Parkville, VIC 3052 Australia E chris.adamson(a)mcri.edu.au<mailto:chris.adamson@mcri.edu.au> www.mcri.edu.au<http://www.mcri.edu.au/> This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication. P Please consider the environment before printing this email

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running -hippo-subfields with both T1 and T2 using FS 6.0
by Alexopoulos, Dimitrios 13 Mar '18

13 Mar '18

I need a clarification with the command to run for generating the hippo subfields on 6.0 using both a T1 mprage and T2 space (both 1mm isotropic). I'd like to run the entire recon-all -all surface and hippo subfields processing stream. Would this be the correct command: recon-all -s subject -i dicom.dcm -hippocampal-subfields-T1T2 T2.nii.gz T1T2 -all Thanks. Jim ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Re: [Freesurfer] Eliminate variable which is the same for all patients from FreeSurfer's Design Matrix
by Douglas Greve 13 Mar '18

13 Mar '18

Hi Kai, please remember to post to the list. Your FSGD file is not quite right. Gender is a discrete variable and should be represented by two groups not as a covariate. If Sequence is discrete, then you need four groups (Gender by Sequence). doug On 3/9/18 3:20 AM, k.ohmstedt(a)stud.uni-heidelberg.de wrote: > Dear Douglas, > > the fsgd file I used is attached. Thank you for your help! > > > Best regards > > Kai > > Zitat von "Douglas N. Greve" <dgreve(a)mgh.harvard.edu>: > >> can you send your fsgd file so that I have a better idea of what you are >> mentioning? >> >> >> On 03/08/2018 08:39 AM, k.ohmstedt(a)stud.uni-heidelberg.de wrote: >>> Dear all, >>> >>> I am trying to correlate psychometric measurements and the local >>> Gyrification Index. >>> To do so, I use the FreeSurfer pipeline to calculate the lGI and then >>> PALM, following the advice in this thread >>> (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-March/050703.ht…) >>> >>> >>> All my subjects are part of the same group, so I used a FSGD with the >>> group "main" to create the design matrix and mask for my data that are >>> required by PALM. >>> Having a closer look at the design matrix that was created, I found >>> that there was a variable for the group that was the same for all my >>> patients. As it is the same for all patients, I thought eliminating it >>> would not be a problem. But after re-running PALM without it, there >>> were huge differences in my results and effects were notably larger >>> and more significant. >>> >>> Do any of you have any experience which option is best in this case? >>> Is it a valid choice to eliminate the variable for the group, as it is >>> the same for each patient anyway? >>> >>> Furthermore, would you recommend centering for the design matrix? I >>> found that this can have an impact, but I am lost on in which cases it >>> should be done and in which it shouldn't. >>> >>> >>> Thank you for your help! >>> >>> >>> Best regards >>> >>> Kai Ohmstedt >>> >>> >>> _______________________________________________ >>> 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] TRACULA -stat coord output file
by Yendiki, Anastasia 12 Mar '18

12 Mar '18

Hi Carissa – These are MNI coordinates. These mean paths are created only for visualizing group results. However the actual FA, etc measures that are used for group analyses are generated in each subject’s native space. Best, a.y From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Carissa Nicole Weis <cnweis(a)uwm.edu<mailto:cnweis@uwm.edu>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Monday, March 12, 2018 at 12:54 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] TRACULA -stat coord output file Hello, Are the contents of the *.coords.mean.txt file generated from the trac-all –stat command, the average MNI coordinates along the tract across subjects? Or average coordinates in native space? Thanks! Carissa

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