[Freesurfer] mri_convert ERROR: could not determine file

Hi there, I am trying to run reg-feat2anat and having a bit of an odd problem. It runs but doesn't produce a anat2exf.register.dat. If I look at the anat2exf.register.dat.fslregister.log file I see right at the beginning it fail with: /data/results/genDIS mri_convert ERROR: could not determine

Re: [Freesurfer] FS 5.2-beta run-times on Amazon Web services (AWS)

Hi Mehul, Thank you for sharing this. Could you include how this would compare to a GPU AWS instance with FreeSurfer's GPU switch? Cheers, -Morgan On Feb 1, 2013, at 6:54 PM, Mehul Sampat wrote: > Hi Folks, > > Just wanted to share our experience with running FS 5.2-beta on Amazon Web > S

Re: [Freesurfer] Freesurfer for canine

I will check with the Emory group that I know has been scanning canines. Don't know if they are interested in the extra work to get FreeSurfer output but since they are doing FMRI maybe they would be OK with sharing their AMRI data. It would be good to ask C. Destrieux on the progress with pig and

[Freesurfer] QAtools errors with aseg QA

Hi there, Just trying out the QAtools and I notice that there are a number of "(standard_in) 1: syntax error" reports for each subcortical label: checking subcortical label: Endosteum, . +/- . (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in)

Re: [Freesurfer] GPU/supercomputer adaptation of freesurfer?

External Email - Use Caution Hi John, I know others (Satra?) might have more recent experience. I used to be able to get recon-all down to about 4 hours. OpenMP made the most difference but the GPU code always helped if you have it running. It really depends on whether you can get

Re: [Freesurfer] GPU/supercomputer adaptation of freesurfer?

External Email - Use Caution Hi Richard, That is a very good point. I knew it was being deprecated and there was talk of OpenCL but I have not been keeping up. Multicore systems were getting the most benefit from newer releases. Certainly, to run the existing CUDA code involved ma

[Freesurfer] cortical mask for group analysis

I would like to make a mask for group analysis that excludes the unknown parcellation area. Since I would like to apply the same mask to all subjects (I have already brought them into alignment with mri_preproc), I was wondering how I can convert the average template label/?h.aparc.annot to a

Re: [Freesurfer] cortical mask for group analysis

Thanks Bruce, Are there any other parcellation units that should be excluded? That seems to be the only white matter PU. Cheers, -Morgan Bruce Fischl wrote: Hi Morgan, no thickness should not be used in the cc. Bruce On Fri, 6 Apr 2007, Morgan Hough wrote: I would like to make a mask

Re: [Freesurfer] cortical mask for group analysis

Bruce Fischl wrote: which parcellation are you using? On Fri, 6 Apr 2007, Morgan Hough wrote: Thanks Bruce, Are there any other parcellation units that should be excluded? That seems to be the only white matter PU. Cheers, -Morgan Bruce Fischl wrote: Hi Morgan, no thickness should not be us

Re: [Freesurfer] cortical mask for group analysis

the vertices and x,y.z of each label, including 'unknown' and 'corpuscallosum' (which are the only two that need excluding). Will that provide you with what you need? Nick On Fri, 2007-04-06 at 21:35 +0100, Morgan Hough wrote: I am using ICA on what would be input to mri_glm

Re: [Freesurfer] cortical mask for group analysis

Thanks Doug, Does a mask.mgh file get written out to the glmdir? Cheers, -Morgan Doug Greve wrote: If you're using glmfit, you can --label $SUBJECTS_DIR/fsaverage/lh.Medial_wall.label --mask-inv Morgan Hough wrote: Hi Nick, I see. I am just not sure how to put this back tog

Re: [Freesurfer] cortical mask for group analysis

I see this does output a mask.mgh which is just what I need. I can convert this and have my nifti mask. Thanks again. Doug Greve wrote: If you're using glmfit, you can --label $SUBJECTS_DIR/fsaverage/lh.Medial_wall.label --mask-inv Morgan Hough wrote: Hi Nick, I see. I am jus

[Freesurfer] aseg visualization question

I have a quick question about an error we are getting with FS 3.0.5 when we are using tkmedit as described in the tutorial to display the segmentations overlaid on the T1. tkmedit good_output brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white -segmentation aseg.mgz The first error seem

Re: [Freesurfer] aseg visualization question

/FreeSurferColorLUT.txt On Thu, 2007-04-12 at 16:54 +0100, Morgan Hough wrote: I have a quick question about an error we are getting with FS 3.0.5 when we are using tkmedit as described in the tutorial to display the segmentations overlaid on the T1. tkmedit good_output brainmask.mgz lh.white

[Freesurfer] quick scatterplot label question

Once I have defined a label in tksurfer and I select *Tools -> *Group* -> Graph Marked Vertices Avg to open a scatterplot window, how do I change the y axis label from the default "external" label. I assume that I need to set this beforehand in the fsgd file but I wasn't sure how. Thanks in adv

[Freesurfer] Making labels from the commandline

I was wondering if I can make a cortical label from a volume ROI from the commandline. I would like to extract thickness values from a region defined in each subject's volume space. Thanks in advance. Cheers, -Morgan ___ Freesurfer mailing list Frees

[Freesurfer] Area measurement question

I just wanted to check which surface was used to compute area and which reference would have this information. Thanks in advance. Cheers, -Morgan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listi

Re: [Freesurfer] Area measurement question

surface you want. I think we also by default compute an ?h.pial.area file. Bruce On Thu, 24 May 2007, Morgan Hough wrote: I just wanted to check which surface was used to compute area and which reference would have this information. Thanks in advance. Cheers, -Morgan

Re: [Freesurfer] Area measurement question

x27;t it? I would rather use the average of the two Bruce On Thu, 24 May 2007, Morgan Hough wrote: Thanks Bruce, These will give quite different values, right? Any chance of getting at the mid-thickness area? Cheers, -Morgan Bruce Fischl wrote: Hi Morgan, you get to choose. I think the

[Freesurfer] mri_vol2surf question

Hi there, I am trying to interpolate a volume of tstats to the average surface with mri_vol2surf but I am getting the error below. Does mri_vol2surf take all the inputs that mri_convert takes? Is this a float2int problem mentioned in the bugs section of the --help? If the latter, what argumen

Re: [Freesurfer] mri_vol2surf question

.mgz file using mri_convert? The error message looks like it can't interpret the file as a NIFTI file (the preceeding float2int message being misleading in this instance, I think). Nick On Tue, 2007-05-29 at 23:27 +0100, Morgan Hough wrote: Hi there, I am trying to interpolate a volume o

Re: [Freesurfer] mri_vol2surf question

tween them or take the max. This type of comparison is always a bit ill-posed because the surface in a 3d talairach imbedding space is not that meaningful. You might try mapping your surface-based results into the talairach volume. doug Morgan Hough wrote: Hi Doug, Multiple versions ar

[Freesurfer] metric distortion questions

Hi there, I would like to ask some questions about metric distortion. 1. Following the Wisco et al (2007) paper, metric distortion is defined as Metric Distortion = k * area of a triangle on a registered sphere / area of triangle on gray/white interface surface which I believe I can compute

Re: [Freesurfer] metric distortion questions

n Tue, 26 Jun 2007, Morgan Hough wrote: Hi there, I would like to ask some questions about metric distortion. 1. Following the Wisco et al (2007) paper, metric distortion is defined as Metric Distortion = k * area of a triangle on a registered sphere / area of triangle on gray/white inte

Re: [Freesurfer] Making labels from the commandline

put a new (linux) version here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_cor2label See the help. I don't know why mri_mergelabels does not work. Is it possible that the tail command is platform dependent? doug Morgan Hough wrote: Hi Bruce, I have

Re: [Freesurfer] Making labels from the commandline

ote: Sorry, should be accessible now. To do what you need, you can just run mri_binarize on the output (or input) of vol2surf. I've put an uptodate copy of mri_binarize there too. doug Morgan Hough wrote: Thanks Doug, I am having some trouble downloading this but the tksurfer interface s

Re: [Freesurfer] Making labels from the commandline

Hi Doug, I see what you mean now. mri_cor2label should do it. Thanks again. Cheers, -Morgan Doug Greve wrote: No, use mri_cor2label to create the label file. I think the 2nd example matches what you want to do. doug Morgan Hough wrote: Hi Doug, Thanks for the ftp fix. I have downloaded

[Freesurfer] another mri_vol2surf question

Hi there, Hopefully a quick question. I was wondering what the del represents in the mri_vol2surf option --projfrac-avg? --projfrac-avg min max del If I use 0 and 1 for min and max, what should del be to average across all the voxels between the two surfaces? Thanks in advance. Cheers, -M

Re: [Freesurfer] another mri_vol2surf question

is to average along the normal. On Thu, 5 Jul 2007, Morgan Hough wrote: Hi there, Hopefully a quick question. I was wondering what the del represents in the mri_vol2surf option --projfrac-avg? --projfrac-avg min max del If I use 0 and 1 for min and max, what should del be to average acros

[Freesurfer] mris_wm_volume

Would it be possible to post binaries of mris_wm_volume again? I believe this is the preferred tool to calculate the total white matter volume over the current aseg output. Thanks in advance. Cheers, -Morgan ___ Freesurfer mailing list Freesurfer@nm

Re: [Freesurfer] mris_wm_volume

: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/dev Nick On Thu, 2007-07-19 at 17:56 +0100, Morgan Hough wrote: Would it be possible to post binaries of mris_wm_volume again? I believe this is the preferred tool to calculate the total white matter volume over the current aseg output. T

Re: [Freesurfer] mris_wm_volume

Hi Bruce, I am afraid the zero is all the output I get. Do I need an updated mris_volume as well perhaps? Cheers, -Morgan Bruce Fischl wrote: that looks like the correct usage. Can you send the entire screen output? On Fri, 20 Jul 2007, Morgan Hough wrote: Hi Nick, Thanks for the tool

Re: [Freesurfer] calculation of total cortical gray matter volume

Hi Bruce, Our subjects don't have this label (?h.cortex) in their label directories. Was this introduced with a recent version? What is the best approximation of this cortical gray matter volume measure for people who have older recons? Cheers, -Morgan Hi Mike, you need to exclude non-co

[Freesurfer] Combining annots?

I have a question about using labels from different annots. The Desikan annot has a large region labeled unknown including medial wall and lateral insula and operculum. The Destrieux annot has a separate medial wall label. Is there an easy way to use the Destrieux annot label of the medial wall

Re: [Freesurfer] mris_wm_volume

NMR at /autofs/homes/010/morgan/con_2878. Cheers, -Morgan Bruce Fischl wrote: works for me. Can you drop the subjects on our site? On Tue, 24 Jul 2007, Morgan Hough wrote: Hi Bruce, I am afraid the zero is all the output I get. Do I need an updated mris_volume as well perhaps? Cheers

[Freesurfer] corpus callosum

I was wondering if I can use the surface area estimate of the aparc corpus callosum label as a decent subject specific measurement of its cross-sectional area. Thanks in advance. Cheers, -Morgan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.

Re: [Freesurfer] corpus callosum

, Morgan Hough wrote: I was wondering if I can use the surface area estimate of the aparc corpus callosum label as a decent subject specific measurement of its cross-sectional area. Thanks in advance. Cheers, -Morgan ___ Freesurfer mailing list

Re: [Freesurfer] mris_wm_volume

emi On Tue, 24 Jul 2007, Morgan Hough wrote: Morning Bruce, I just checked this on a subject you already have there. I get the same result at NMR with this subject using the dev version of mris_wm_volume from /usr/local/freesurfer/dev/bin/mris_wm_volume which I think is the best match for the

Re: [Freesurfer] mris_wm_volume

Hi Bruce, That did it. Great. The output is mm^3? Thanks again. Cheers, -Morgan Bruce Fischl wrote: oops, there should only be one --in_center on the cmd line (followed by 0 0 0 ) On Tue, 24 Jul 2007, Morgan Hough wrote: Hi Bruce, I try this in $subject/mri but I get the following

[Freesurfer] Partitioning GM/WM boundary surface

I would like to obtain a ratio of gyral/sulcal GM/WM boundary surface area. I was wondering if the best solution would be to threshold each subject's ?h.sulc files to form a label that contains all gyral areas and then use mris_anatomical_stats -l to constrain a surface area measurement to this

Re: [Freesurfer] Partitioning GM/WM boundary surface

om the old recon-all output? Cheers, -Morgan Bruce Fischl wrote: Hi Morgan, yes, that seems reasonable. You can start with the ?h.cortex.label and subdivide it into sulcal and gyral to avoid the medial wall. cheers, Bruce On Tue, 24 Jul 2007, Morgan Hough wrote: I would like to obtain a rati

Re: [Freesurfer] Partitioning GM/WM boundary surface

mris_make_surfaces and it will create them (and not deform the surface in regions outside the label) On Wed, 25 Jul 2007, Morgan Hough wrote: Hi Bruce, These subjects were run with an older version of FreeSurfer and don't have ?h.cortex.label. I am afraid I don't see a generating comma

[Freesurfer] mri_segstats question

Hi , I would like to use mri_segstats with an aprac parcellation to get the mean/stddev of the norm.mgz intensities by parcel. I have tried the following usage: mri_segstats --annot con_2304 lh aparc --ctab-default --nonempty --excludeid 0 --sum con_2304.norm.aseg.sum --in $SUBJECTS_DIR/con

[Freesurfer] Banks of the superior temporal sulcus question

I was just wondering why the banks of the superior temporal sulcus was made into its own label on the Desikan template. Does this correspond (roughly) to a particular functional area. I didn't see anything in the paper about why it was chosen. Is it just easy to define given sulcal/gyral bounda

Re: [Freesurfer] Banks of the superior temporal sulcus question

l AD. On Mon, 6 Aug 2007, Morgan Hough wrote: I was just wondering why the banks of the superior temporal sulcus was made into its own label on the Desikan template. Does this correspond (roughly) to a particular functional area. I didn't see anything in the paper about why it was chosen.

[Freesurfer] mris_anatomical_stats question

I am reporting thickness values from subjects native space constrained by mask labels using mris_anatomical_stats. I am currently getting the average of the unsmoothed estimates. I would like to be able to get smoothed values but the usage reports the smoothing option as -nsmooth <#> where the

[Freesurfer] High-resolution limits of FS4

Hi there, I just wanted to check on the spatial resolution limits of FS4. Is it possible to process a whole-brain, 0.5mm isotropic voxel size volume without downsampling it? Thanks in advance. Cheers, -Morgan ___ Freesurfer mailing list Freesurfer@

[Freesurfer] Sulcal CSF measure

Hi there, I was wondering if sulcal CSF differences should be reported given the difficulty in its identification from T1 data? How is sulcal CSF defined by FS? Thanks in advance for your time. Cheers, -Morgan ___ Freesurfer mailing list Freesurfer

[Freesurfer] recon-all error

I downloaded the latest freesurfer-dev and I was testing out my install with "recon-all -autorecon-all -subjid bert" and I am getting this error. mri_convert nu4.mnc nu.mgz mincRead(): can't find file /var/scratch11/mhough/subjects/bert/mri/nu4.mnc reading from nu4.mnc... ERROR: converting nu to C