[Freesurfer] synthstrip error

External Email - Use Caution Hi, I am passing synthstrip an nii.gz file, and it keeps giving the error "ValueError: cannot determine file format from extension for test " (full error below). Any suggestions on how to fix this issue? The nifti files was made from dicom images

Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

eprocess > that brain and see if that happens again. > > Hope this helps, > > best, > > Alan > > > > On Thu, Apr 13, 2017 at 4:49 PM, Salil Soman <s...@jhu.edu> wrote: > >> Hi, >> >> I have run a number of cases through the FS6 hippocampal

[Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

time to collect the results, I find I have many more lh.hippoSfVolumes-T1.long.v10.txt (67) than rh.hippoSfVolumes-T1.long.v10.txt files (25). Any suggestions on what I may be doing incorrectly? Thanks! Salil Soman ___ Freesurfer mailing list Freesurfer

[Freesurfer] How best to review actual anatomic structures labelled under hippocampal subfield label?

. Best wishes, Salil Soman, MD, MS ___ 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

Re: [Freesurfer] freesurfer in patients with brain volume loss after old injury or infarcts

Hi, Is there an official thought on using freesurfer on cases were there is volume loss after old stroke, or surgery, or trauma? I have a number of cases were the results in general look reasonable for the remaining brain tissue, and was was wondering if it is valid to use that data for analyses?

[Freesurfer] using merge_stats_tables to merge broadman areas for multiple subjects.

Hi, Following earlier device from this list, I was able to run the merge_stats_tables command for a single subject as so: merge_stats_tables --inputs $SUBJECTS_DIR/SUBJ_ID1/stats/lh.BA.stats --all-segs --tablefile test_lh_BA_Stats_volumes.txt --meas volume But when I tried to pass a series of

[Freesurfer] Possible to generate table of statistics for specific label?

Dear List Members, Is it possible to generate tables of volume / area / thickness information for a specific label that is not included in aparcstats or asegstats using command line code in freesurfer (e.g. the broadman areas)? If so, could someone point me to the instructions? Thank you for

[Freesurfer] Fwd: Freesurfer Digest, Vol 131, Issue 13

@nmr.mgh.harvard.edu Message-ID: 54aeb237.9010...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=windows-1252; format=flowed Yep, you can use somehting like mri_segstats --i lh.thickness --slabel subject lh lh.BA3a.label --id 1 --sum table.dat doug On 01/08/2015 08:50 AM, Salil Soman wrote

[Freesurfer] freesurfer gpu acceleration using amd video cards?

Dear List Members, Does anyone know if it is possible to use freesurfer gpu based acceleration using amd video cards? Thanks, Salil Soman, MD, MS ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman

Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences

Dear Doug, Thank you for your email. On Wed, Sep 24, 2014 at 8:57 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: 2) While most of the CBF to T1 registrations using the transformation for the PD to the T1 image worked reasonably, there are a few where the registration is a little off

Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences

-erode. On 09/18/2014 04:43 PM, Salil Soman wrote: Dear Doug, Thank you for your email. The registration overlap looks reasonable. Thank you for considering this question. Best wishes, Sal On Thu, Sep 18, 2014 at 12:14 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr

Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences

? Does it overlay correctly on the T1.mgz? doug On 09/14/2014 11:40 PM, Salil Soman wrote: Thank you Doug. I am having trouble with extracting statistics using this method. I am able to use bbregister to get a transformation that registers the PD image of the ASL to the T1. I then used

Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences

wishes, Salil Soman, MD, MS On Sun, Sep 14, 2014 at 3:32 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: yep, you can use it for anything. doug On 9/14/14 12:52 PM, Salil Soman wrote: Dear Doug, Thank you again for this email. Do you think it is possible to use this method

[Freesurfer] Any good cortical segmentation methods for brains with infarct or tumors?

Hi, Does anyone have recommendations for good automated cortical segmentation tools for brains with infarct (so some brain missing) or tumors? I am under the impression that FreeSurfer is not reliable in these cases. If I am incorrect, any pointers on how to use FreeSurfer in these cases would

[Freesurfer] Freesurfer longitudinal GLM Design question

Hi, I have been following the tutorial from here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial and here: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel And I believe I am running into problems with my GLM design. I have a set of subjects with 2

[Freesurfer] longitudinal QDEC question

and time point 2. I am a little unclear on what the explanatory variable should be performing this analysis. Any suggestions on how best to structure the analysis would be greatly appreciated. Best wishes, Salil Soman, MD, MS ___ Freesurfer mailing list

[Freesurfer] question about qdec Stats Data Import for Longitudinal Workflow

When following the longitudinal qdec tutorial ( https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel), does using the generate Stats Data Tables option extract data for the difference between time point1 and 2, or something else? Thank you. Salil Soman, MD, MS

[Freesurfer] how to pass openmp option to mri_cvs_register through Tracula-prep?

Hi, I noticed that openmp is set to 1 in mri_cvs_register. However, I do not see a way to pass on this parameter to to mri_cvs_register through dmrirc for tracula - prep. Can anyone point me to how this can be done? Thanks! Sal ___ Freesurfer mailing

[Freesurfer] possible to enable openmp with tracula cvsreg?

Hi, I noticed in the output for tracula -prep I am currently running using cvsreg it mentions openmp=1, I was wondering if there is a way to enable more than 1 core for openmp for tracula-prep? Thanks, -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences

[Freesurfer] tracula cvs_reg taking greater than 24 hours

=0.000573: new neg 23004, old_neg 23842, delta 838, rms=0.766 (0.745%) Numerical result out of range -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans

[Freesurfer] What coordinate space is freesurfer output in?

Hi, I was wondering what the default freesurfer coordinate space is called? (MNI, something else)? Thanks, Sal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in

[Freesurfer] possible to see an example of phase map input for tracula?

Hi, Could someone point me to an example for a sample phase map that tracula can take as input? We do not have a specific sequence for this on our GE system but may be able to output it from some of our 3D GRE sequences. Best wishes, -- Salil Soman, MD, MS Postdoctoral Research Fellow

[Freesurfer] possible to do multi planar reformats of hippocampal subfields in freeview?

Hi, I am reviewing hippocampal subfield segmentation using freeview, and was wondering if there is a way to do multiplanar reformats so I can get reorient the cor/sag/axial planes to that of the hippocampus? Thank you. -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological

[Freesurfer] possible to render hippocampal subfield segmentations as 3D structures?

wishes, -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System

Re: [Freesurfer] possible to render hippocampal subfield segmentations as 3D structures?

isosurface as well, since the default is gray. You need to be in the 3D view in order to display isosurfaces. -Louis On Thu, 6 Feb 2014, Salil Soman wrote: Hi, I generated hippocampal subfield segmentations, can generate statistics, but was wondering if there was a way to visualized

[Freesurfer] Tracula shows some tracks with bbr and others with flt

Hi, I have a couple of dti cases where bbr will include forceps major and missing forceps minor and flt will be the opposite. Similar things have occurred for anterior thalamic tracts and cingulum bundles. Any suggestions on what I may be doing incorrectly? Best wishes, Sal

Re: [Freesurfer] Tracula only outputs merged flt file (and missing bbr)

there are subdirectories with path.pd.nii.gz files for all the tracts? Does the trac-all.log show any commands run or error messages for the bbr case? a.y On Sat, 18 Jan 2014, Salil Soman wrote: Hi, Is there a specific issue to troubleshoot if Tracula only creates the merged ... flt file

[Freesurfer] Outputting all tracula statistics to table

Hi, What is the proper way to generate a single table containing all tracula generated statistics for all subjects in a study? I tought tractstats2table was the way to do this, I am confused as to how trac-all -stat factors into this process in the latest (12-09-13 version)? Thank you. -Sal

[Freesurfer] Tracula only outputs merged flt file (and missing bbr)

Hi, Is there a specific issue to troubleshoot if Tracula only creates the merged ... flt file and not the merged ... bbr file in paths? All of my dmrirc files have both bbr and flt =1, and most of my outputs have both, but occasionally I only get 1. Thanks! -- Salil Soman, MD, MS Postdoctoral

[Freesurfer] Fwd: Re: problem with bvecs file with new (12/13) TRACULA code

-- Forwarded message -- From: Salil Soman salso...@stanford.edu Date: Jan 12, 2014 1:28 PM Subject: Re: problem with bvecs file with new (12/13) TRACULA code To: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu Cc: Hi, Thank you for your email. Taking the .bval and bvec files

[Freesurfer] problem with bvecs file with new (12/13) TRACULA code

files have non-matching number of entries. I do have the dorotbvecs option set to 1 (as I had before). Any suggestions on what I am doing incorrectly would be greatly appreciated. I have attached the bvec and bval files I am providing a input. Best wishes, Sal -- Salil Soman, MD, MS Postdoctoral

Re: [Freesurfer] longitudinal hippocampal subfields analysis

Thank you Martin. I will try this approach. I was able to temporarily move the longitudinal subject data to its own folder to run aparc2table and aseg2table. Hopefully this will also work for the hippocampal subfield script. Best wishes, Sal Salil Soman, MD, MS Postdoctoral Research Fellow

[Freesurfer] longitudinal hippocampal subfields analysis

point me to how to perform this analysis, as kvlQuantifyHippocampalSubfieldSegmentations.sh does not work on the output files I've generated. Thank you. Salil Soman, MD, MS ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] possible to run freeview using other versions of libjpeg.so.62?

Hi, My cluster environment is setup to use libjpeg turbo on ubuntu 13.04 (ends up with libjpeg.so.8.0.2 in the /usr/lib/x86_64-linux-gnu/ directory). Is it possible to use this version of libjpeg to run freeview (it currently complaints that it cannot find libjpeg.so.62)? If so, can anyone

[Freesurfer] Change in Tracula ability to use bvec / bval file containing zeros for b0 images?

in the diffusion tutorial do include the b0 0. Does the current version of tracula require the b0 entries to be removed? If not, any suggestions on what I may be doing incorrectly would be great. Thank you. Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow

[Freesurfer] Units for Aparcstats2table for thickness and curvature

Hi, I am writing to confirm the units for aparcstats2table for thickness and thicknessSTD are mm, and curvature is radians. It would be a great help if this could be confirmed. Thank you. Salil ___ Freesurfer mailing list

Re: [Freesurfer] kvlQuantifyHippocampalSubfieldSegmentations Usage

Hi, Have been able to run kvlQuantifyHippocampalSubfieldSegmentations.sh to get hippocampal subfield segmentation number of voxels. How do I convert these values into volumes? I am guessing the voxel size of the original image is not the correct conversion factor. Also, I have not been able to

[Freesurfer] How to get aparcstats2table to output thickness and other parameters

Hi, Is there a way to get aparcstats2table to output all of the information for each subject, including thickness values? Thank you, Salil ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Fwd: Minimum Dti directions and odf

Hi, I hope all is well. Was wondering if any of had heard of an explicit minimum number of DTI directions necessary for using odf / hardi modeling ? I have run a couple of data sets of 30 directions (+ 5 b0) through TRACULA, and have run this same data through diffusion toolkit using the hardi /

Re: [Freesurfer] Longitudinal freesurfer analysis question

series. It seems that you did not run your images through the longitudinal stream if your etiv is different across time points. For longitudinal processing see here: http://freesurfer.net/fswiki/LongitudinalProcessing Bes,t Martin On Nov 10, 2013, at 3:37 PM, Salil Soman salso

[Freesurfer] Etiv difference in difference in same patient

Hi, My understanding of etiv is that it is derived from the registration of a brain to atlas space and not actually derived from the freesurfer segmentation. I have a set of patients imaged at 2 time points that all have different etiv values between the first and second scan that are

[Freesurfer] Clarification regarding bvec processing in TRACULA

Hi, After much searching, it appears to be pretty uniform that the product DTI sequence performed on GE requires the y gradient to be flipped. For the datasets with which I am working diffusion toolkit, vistalab and exploredti all require the y gradient to be flipped. However, Tracula makes

[Freesurfer] gradient table question for Tracula

need to have the Y component flipped for my GE acquisitions or is this adjusted in the tracula processing? Thank you. -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology

Re: [Freesurfer] freeview problem

line does a window popup displaying spinning gears? -Zeke On 08/16/2013 05:55 AM, Salil Soman wrote: Hi, When I try to run freeview on my ubuntu 13 machine, running the nvidia 5.0 cuda drivers, I get the following errors: Xlib: extension NV-GLX missing on display localhost:10.0

[Freesurfer] freeview problem

Hi, When I try to run freeview on my ubuntu 13 machine, running the nvidia 5.0 cuda drivers, I get the following errors: Xlib: extension NV-GLX missing on display localhost:10.0. Xlib: extension NV-GLX missing on display localhost:10.0. Xlib: extension NV-GLX missing on display

[Freesurfer] hippocampal subfields question

Hi, I just wanted to confirm that label hippocampus in the hippocampal subfields segmentation is simply parts of the hippocampus that do not fall into one of the other major categories? Also, where can I find the units for the hippocampal subfields? I am seeing some discrepancy between the left

[Freesurfer] preferred method for generating appropriate bvecs for tracula

Hi, I have dicoms that I turn to nifti using dcm2nii (with the default settings plus anonymization option turned on [-a y]). The bvec files it generates by default are 3 rows by n columns (where n is b0 number + directions). I am under the impression tracula requires this to be converted to a n

Re: [Freesurfer] preferred method for generating appropriate bvecs for tracula

] @ k = $k + 1 end I'd make sure though dcm2nii doesn't L-R flip the gradient vectors, I think there was a thread recently that suggested it might. On Wed, 7 Aug 2013, Salil Soman wrote: Hi, I have dicoms that I turn to nifti using dcm2nii (with the default settings plus anonymization

Re: [Freesurfer] preferred method for generating appropriate bvecs for tracula

Thank you for your response. Is there a best way to review the eigenvectors (tkmedit, freeview, other program?). Thank you. -S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Best way to generate Complete Stats Table

If not, I do not see a file called mri/hippsubfieldseg.mgz for my output, and any advice on where I could find it would be great. Best wishes, Sal -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study

Re: [Freesurfer] Best way to generate Complete Stats Table

the seg volume and the LUT doug On 08/06/2013 03:09 PM, Salil Soman wrote: On Mon, Aug 5, 2013 at 2:22 PM, Douglas Greve gr...@nmr.mgh.harvard.edumailto: gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu wrote: mri/hippsubfieldseg.mgz Thank you Doug. Just to clarify the code you

Re: [Freesurfer] Best way to generate Complete Stats Table

the volumeStats_left.txt and volumeStats_right.txt files in the mri subdirectory. Again, any pointers on how to generate group stats into a table would be a great help. Best wishes, Sal On Tue, Aug 6, 2013 at 12:33 PM, Salil Soman salso...@stanford.edu wrote: Hi Doug, I realize now that I was unclear

Re: [Freesurfer] Best way to generate Complete Stats Table

), and then the script worked and generated the 2 summary files. Best wishes, Sal On Tue, Aug 6, 2013 at 12:40 PM, Salil Soman salso...@stanford.edu wrote: I can add that after running kvlQuantifyHippocampalSubfield Segmentations.sh I cannot find the nonPartialVolumeStatsLeft.txt

Re: [Freesurfer] Best way to generate Complete Stats Table

cheers Bruce On Sun, 4 Aug 2013, Salil Soman wrote: Hi, I have a large dataset for which I run freesurfer and confirmed that the apar+aseg.mgz file is satisfactory. Can someone please recommend the best way to aggregate all of the volumes/other values generated by freesurfer into a single

[Freesurfer] tksurfer and mountain lion problem / question

Hi, I can run freeview using my current install on Mountain Lion, however when I run tkmedit or tksurfer I get the following error: GLUT: Fatal Error in tksurfer.bin: could not open display: :0.0 my /etc/profile has the setting export DISPLAY=:0.0 for a different program. Is there settings I

Re: [Freesurfer] Best way to generate Complete Stats Table

/FreeSurferColorLUT.txt You can then run asegstats2table specifying hipposub.stats as the stats file doug On 8/5/13 3:39 PM, Salil Soman wrote: Dear Doug and Bruce, Thank you for your emails. I have also run the -hippo-subfields option on my freesurfer processing. How do I extract those

[Freesurfer] Best way to generate Complete Stats Table

Hi, I have a large dataset for which I run freesurfer and confirmed that the apar+aseg.mgz file is satisfactory. Can someone please recommend the best way to aggregate all of the volumes/other values generated by freesurfer into a single table for this dataset? (e.g. subjects as Rows and values

Re: [Freesurfer] Best way to generate Complete Stats Table

Thank you Doug! -S On Sun, Aug 4, 2013 at 10:09 AM, Douglas Greve gr...@nmr.mgh.harvard.eduwrote: use asegstats2table and aparcstats2table. This will give you 3 tables which you could then merge into 1. doug On 8/4/13 12:22 PM, Salil Soman wrote: Hi, I have a large dataset for which

Re: [Freesurfer] possible to use multiple B value DTI in Tracula?

Soman wrote: Hi, I was wondering - is it possible to use DTI data of multiple B values in Tracula (acquired during the same session and same TE)? Best wishes, Sal Salil Soman, MD, MS The information in this e-mail is intended only for the person to whom it is addressed. If you believe

[Freesurfer] possible to use multiple B value DTI in Tracula?

Hi, I was wondering - is it possible to use DTI data of multiple B values in Tracula (acquired during the same session and same TE)? Best wishes, Sal Salil Soman, MD, MS ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] average/RB_all_2008-03-26.gca not found error

be greatly appreciated. Best wishes, Sal Hi Salil what is FREESURFER_HOME set to? Is it /usr/local/freesurfer? Does /usr/local/freesurfer/average/**RB_all_2008-03-26.gca exist? cheers Bruce On Mon, 8 Jul 2013, Salil Soman wrote: Hi, Am running this command: $FREESURFER_HOME/bin/recon-all -i

Re: [Freesurfer] color scale for longitudinal analysis using freeview

Dear experts, Could someone point me to the color key for the output of the longitudinal analysis as viewed in freebies (as generated by the freesurfer longitudinal analysis tutorial)? Thank you, Sal Salil Soman, MD, MS ___ Freesurfer mailing list

[Freesurfer] average/RB_all_2008-03-26.gca not found error

Hi, *Am running this command:* $FREESURFER_HOME/bin/recon-all -i 3DSPGR.nii.gz -s WCA_248_T1Q_FS -nuintensitycor-3T -nocanorm -openmp 50 -hippo-subfields -use-cuda -all *And am get this out put / error:* Testing for CUDA device: nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2012

Re: [Freesurfer] NU_evaluate crash while running Longitudinal Analysis with FS 5.3

(base). Next time please send the recon-all.log file (from the subject's scripts directory). It gives us more information than just the screen output. Best, Martin On Jul 4, 2013, at 1:17 AM, Salil Soman salso...@stanford.edu wrote: Hi, I have been trying to run the FS longitudinal

[Freesurfer] NU_evaluate crash while running Longitudinal Analysis with FS 5.3

= 768), see attached log. Any suggestions on what I am doing incorrectly? Best wishes, Sal Salil Soman, MD, MS RZ_1484_LONG_POST.o893489 Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu

[Freesurfer] CUDA Error when runnign freesurfer

Hi, I am running freesurfer 5.3 on an ubuntu 13.04 with a nvidia card and the the CUDA drivers installed. I am getting the following error when I try using the use-cuda command: Testing for CUDA device: nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2012 NVIDIA Corporation Built on

[Freesurfer] Possible to generate connectivity map using FS and Tracula

Dear Doug, Is there a way to use the Freesurfer and Tracula output to compute connectivity maps? Thanks! Sal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in

Re: [Freesurfer] possible to display data obtained through mri_segment as heatmap?

me know if you need pointers doug On 06/01/2013 04:43 PM, Salil Soman wrote: Dear Doug, Thank you for your response. I am not sure I understand what I would be overlaying. I would like to display the T1 volume for the subject, but for each voxel color value, I would like that to reflect

Re: [Freesurfer] possible to display data obtained through mri_segment as heatmap?

to do this in freeview. Any pointers to further details would be greatly appreciated. Best wishes, Sal On Fri, May 31, 2013 at 12:46 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: you can just specify an overlay on the freeview command line On 05/31/2013 03:26 PM, Salil Soman wrote: I

[Freesurfer] possible to display data obtained through mri_segment as heatmap?

Dear Doug, Thank you for your recent advise with using freesurfer to extract mean values from non structural image data. Is there a way to generate an image (e.g. heat map) displaying those values in free view? Best wishes, Sal ___ Freesurfer mailing

Re: [Freesurfer] possible to display data obtained through mri_segment as heatmap?

? On 05/31/2013 03:20 PM, Salil Soman wrote: Dear Doug, Thank you for your recent advise with using freesurfer to extract mean values from non structural image data. Is there a way to generate an image (e.g. heat map) displaying those values in free view? Best wishes, Sal -- Douglas N. Greve

Re: [Freesurfer] no hippocampal stats despite running FS 5.3 with -hippo-subfields

to make a separate call)? recon-all -i SPGR/*.gz -s SUBJECTIDENTIFIER -nuintensitycor-3T -nocanorm -openmp 50 -hippo-subfields -all Thank you, Sal On Sun, May 26, 2013 at 2:33 PM, Salil Soman salso...@stanford.edu wrote: Dear Freesurfer Experts, I have been running freesurfer 5.3 without any

Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences

gr...@nmr.mgh.harvard.eduwrote: On 5/26/13 2:11 PM, Salil Soman wrote: Dear Doug, Thank you for your email. Following up on our previous discussions: 1) *bbregister fail *- this was happening because of error from fslregister. The variable fsvol was translating to ERROR. In fslregister

Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences

: On 5/25/13 1:39 PM, Salil Soman wrote: Thank you Doug. Just so I am clear - is the anatomical the nifti T1.mgz or is it a different file. From your email I gather should do the following: *1) Use bbregister to register the lowb image to the anatomical. This creates a registration matrix

Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences

mri/aparc+aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i Vol_906_Reg_Bold.nii --sum Vol_906_aparc_aseg.stats Thanks! -S On Sun, May 26, 2013 at 11:11 AM, Salil Soman salso...@stanford.edu wrote: Dear Doug, Thank you for your email. Following up on our previous discussions: 1

Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences

As I am working with a 3D volume and not an ADC map, should I still use --seg-erode 1 with mr segstats? Thank On Sun, May 26, 2013 at 1:11 PM, Salil Soman salso...@stanford.edu wrote: Hi - I realize that the --inv tag was still in my commands for mr_vol2vol (causing the target and the moving

[Freesurfer] no hippocampal stats despite running FS 5.3 with -hippo-subfields

(as described on http://ftp.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation), I do not find any of them. Any suggestions on what I am doing incorrectly? Best wishes, Salil Soman, MD, MS ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences

a registration matrix. Use mri_vol2vol and the registration to map the ADC map to the anatomical, then use mri_segstats to extract the values doug ps. Please post questions to the FS list instead of us directly so that others can benefit and it gets archived. thanks! On 5/25/13 1:03 PM, Salil Soman

[Freesurfer] Fwd: BBR Register failing

-- Forwarded message -- From: Salil Soman salso...@stanford.edu Date: Sat, May 25, 2013 at 8:00 PM Subject: BBR Register failing To: Douglas N Greve gr...@nmr.mgh.harvard.edu Dear Doug, I attempted to run the process we discussed earlier today for registering a different tissue

Re: [Freesurfer] BBR Register failing

, May 25, 2013 at 8:23 PM, Douglas Greve gr...@nmr.mgh.harvard.eduwrote: Hi Sal, can you post this to the list instead of me directly? thanks! doug On 5/25/13 11:00 PM, Salil Soman wrote: Dear Doug, I attempted to run the process we discussed earlier today for registering

Re: [Freesurfer] BBR Register failing

) Any suggestions would be a huge help. -Sal On Sat, May 25, 2013 at 8:35 PM, Salil Soman salso...@stanford.edu wrote: Done. Thank you for your consideration. The best I can figure so far is 1) the script's attempt to make the tmp.bbregister.7392 directory fails and 2) (after I manually make

[Freesurfer] recon-all with multiple spgr's per subject

Dear Freesurfer experts, Could someone point me to the syntax for having recon-all use multiple T1 volumes for the same subject (which I believe it is supposed to motion correct and average). Thanks, Salil Soman, MD, MS ___ Freesurfer mailing list

[Freesurfer] FS 5.2 asegstats2table is not found or is too small to be a valid stats file error

Dear Experts, I am trying to extract FS 5.2 statistics for a single subject using the following command: asegstats2table --subjects SUBJECTNAME --tablefile teststats.txt I keep getting *the following error: * *The stats file /PATH/SUBJECTNAME/stats/aseg.stats is not found or is too small to

Re: [Freesurfer] bbr problem run

PM, Salil Soman salso...@stanford.edu wrote: Thank you for your response. I tried re-running Tracula using bbr in a subject I had successfully run using flt. trac-all prep and bedp worked without an error. Bedpostx sent me an email confirming bedpost completed without problem. However, when I

[Freesurfer] corRead() error with Tracula / FS 5.2

be greatly appreciated. Best wishes, Salil Soman ___ 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

[Freesurfer] Tracula on cluster problem

slices processed Queuing post processing stage /mnt/glusterfs/myaccount/freesurfer/bin/bedpostx_seychelles: line 376: 14275 Terminated ${subjdir}.bedpostX/monitor Any suggestions on what I am doing incorrectly? Thank you, Salil Soman, MD, MS

[Freesurfer] Clarification regarding eTIV

Dear List Members, I am planning to use the eTIV for a group analysis using segmentation volumes and I need to confirm that the eTIV ( aka ICV) generated in freesurfer is NOT dependent on the skull strip? Specifically, I wanted to make sure one does not need to QC the skull strips to make sure

[Freesurfer] Outputting reformatted images in freesurfer

are applied to the images by the .reg file) The end result I'm looking for is that is both images are loaded into freesurfer with a reg file that applies no transforms, the images will be the same as though the original .reg file was used. Thanks, Salil Soman [EMAIL PROTECTED

[Freesurfer] Using overlay in Freesurfer

by mri_convert from spm files. Thanks, Salil Soman [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Problem with overlay of EPI analyze volume over T1 analyze volume in free surfer

to be properly formed, as I can read it directly into freesurfer and get a properly formed image. Was wondering if anyone had any suggestions as to what may be going wrong? Thanks, Salil Soman [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer