Re: [Freesurfer] Morphing Buckner2011 MNI152 to subject's space {Disarmed}

[Katherine Damme]

External Email - Use Caution

Hello,

I have a tone of FS people who have been run through Recon-all and I am
happy with the output but I would like to expand the existing labels to
include the Buckner 7 tight labels. Is this still the best way to update my
subject labels to include these labels?

On Sat, Nov 26, 2016 at 8:07 PM Thomas Yeo  wrote:

> Hi Noam,
>
> This should be a two step procedure, rather than a one-step procedure.
> Here's a previous email I sent to the list about warping Choi's
> striatum atlas to individual subject's striatum (which I have modified
> for the cerebellum for you). Let us know if this works.
>
> 1) Assuming you are quite happy with the freesurfer cerebellum
> parcellation in your subjects, then I am assuming freesurfer nonlinear
> registration (talairach.m3z) is working quite well. Talairach.m3z
> warps your subject to an internal freesurfer space (kinda like MNI305,
> but not quite). Let's say the freesurfer recon-all output is at
> /SUBJECT_FS/
>
> 2) Run the MNI152 1mm template (the one from FSL) through recon-all.
> Recon-all will give you a Talairach.m3z that allows you to map the
> MNI152 1mm template to the internal freesurfer space. Let's say the
> freesurfer recon-all output is at /MNI152_FS/
>
> 3) Then do the following:
>
> a) Use mri_vol2vol to upsample the Buckner cerebellum atlas which is
> 2mm resolution to the 1mm MNI152 template:
>
> >> mri_vol2vol --mov Buckner_atlas.nii.gz --targ MNI152/mri/norm.mgz
> --regheader --o Buckner_atlas1mm.nii.gz --no-save-reg --interp nearest
>
> Notice that I use norm.mgz of the MNI template rather than the
> original MNI template. norm.mgz is the 256 x 256 x 256 conformed
> version of the MNI template that recon-all puts through.
>
> b) warp the Buckner_atlas1mm.nii.gz to freesurfer nonlinear volumetric
> space:
>
> >> setenv SUBJECTS_DIR 
> >> mri_vol2vol_used --mov Buckner_atlas1mm.nii.gz --s MNI152_FS --targ
> $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o
> Buckner_atlas_freesurfer_internal_space.nii.gz --interp nearest
>
> c) warp the Buckner_atlas_freesurfer_internal_space.nii.gz to your subject:
>
> >> setenv SUBJECTS_DIR 
> >> mri_vol2vol --mov $SUBJECTS_DIR/SUBJECT_FS/mri/norm.mgz --s SUBJECT_FS
> --targ Buckner_atlas_freesurfer_internal_space.nii.gz --m3ztalairach.m3z
> --o Buckner_atlas_subject.nii.gz --interp nearest --inv-morph
>
> This is not optimal because of the double interpolation. You might
> want to use the MNI template instead of the Buckner_atlas to test the
> above, so you can check the goodness of the warp. The final warped MNI
> template should hopefully look identical to your subject. If that
> works, then use the Buckner_atlas. Note that mri_vol2vol does not work
> properly for talairach.m3z below version 5, so you should use version
> 5x mri_vol2vol.
>
> Regards,
> Thomas
>
> On Thu, Nov 24, 2016 at 6:31 AM, Peled, Noam 
> wrote:
> > Dear group,
> > I'm trying to morph the Buckner2011 cerebellum segmentation map from
> MNI152
> > to subject's space:
> > mri_vol2vol --mov subjects/sub01/mri/norm.mgz --s sub01 --targ
> > Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
> --m3z
> > talairach.m3z --o sub01_Buckner2011_atlas_17_loose.nii.gz --nearest
> > --inv-morph
> > It worked with the 17 networks, but didn't work with the 7 networks
> version.
> > Any ideas? This is really strange.
> >
> > Thanks,
> > Noam
> > (function(){(function n(e) { "use strict"; function t(e) { if
> (e.parentNode)
> > if (e.childNodes.length > 1) { for (var t =
> > document.createDocumentFragment(); e.childNodes.length > 0; ) { var n =
> > e.childNodes[0]; t.appendChild(n); } e.parentNode.replaceChild(t, e); }
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> > e.parentNode.removeChild(e); } function n(e) { if (e) try { for (var n =
> > e.querySelectorAll(".gr_"), r = n.length, o = 0; r > o; o++) t(n[o]); }
> > catch (i) {} } function r(e) { try { Object.defineProperty(e,
> "innerHTML", {
> > get: function() { try { var t = e.ownerDocument.createRange();
> > t.selectNodeContents(e); var r = t.cloneContents(), o =
> > document.createElement("div"); return o.appendChild(r), n(o),
> o.innerHTML; }
> > catch (i) {} }, set: function(t) { try { var n =
> > e.ownerDocument.createRange(); n.selectNodeContents(e),
> n.deleteContents();
> > var r = n.createContextualFragment(t); e.appendChild(r); } catch (o) {} }
> > }); } catch (t) {} } if (e) { var o = e.cloneNode; e.cloneNode =
> function(t)
> > { var i = o.call(e, t); if (e.classList.contains("mceContentBody"))
> > i.innerHTML = e.innerHTML, n(i); else try { r(i); } catch (a) {} return
> i;
> > }, r(e); }
> >
> })(document.querySelector("[data-gramm_id='d22b74fd-b802-72ef-9275-81341a576398']"))
> > })()
> >
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> >
> >
> > The 

[Freesurfer] Mean FA values for major tracts all greater than 1

[Katherine Damme]

External Email - Use Caution

Hello Freesurfer Support group,

I have run tracula on hundreds of subjects for a study and their primary
tracts are all showing that MFA is greater than 1. Typically, I expected
that MFA should be in the .3 to 1 range. Should I be suspicious that these
MFA values are over the top of that range or is this common for major
tracts like the forceps major?

Thank you for your insights on this potential error.

Kate
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[Freesurfer] FreeSurfer Labels To Diffusion Toolkit/TrackVis

[Katherine Damme]

Hello Everyone,

I would like to use the FreeSurfer labels for fMRI and DTI in graph theory
analyses. I am attempting to use UMPC  to
generate the graphs, which requires that the diffusion tensor imaging be in
.dtk form. However, I have been struggling to get the FreeSurfer labels
into the .dtk space.

While I have found this
website
suggesting a method for moving from the dtk space to FreeSurfer, it doesn't
appear to be a reversible process.

Leading me to ask:

1. Is there a way to generate graphs from TRACULA?

or

2. How can I transform the labels or dlabels into dtk space?

Thank you for any help on this topic!

Kate Damme
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[Freesurfer] Extracting lgi cluster values over label

[Katherine Damme]

Hello Everyone!

I have run LGI analyses according to the JoVE article:
https://www.jove.com/video/3417/how-to-measure-cortical-folding-from-mr-images-step-step-tutorial-to

I created labels from the significant clusters and would like to
extract the lgi values from these labels and found that past email
chains suggested the following:

>>>* mris_anatomical_stats -l ?h_lgi_significant_cluster.label -t 
>>>**SUBJ/surf/?h.pial_lgi -f ${subj}/stats/?h.aparc_lgi.stats **${subj}** 
>>>?h*>>>* aparcstats2table --subjects ALL_YOUR_SUBJECTS --hemi ?h --meas 
>>>thickness** --parc aparc_lgi --tablefile aparc_lgi_?h.txt*


*However the output results in a stats table with the following headings:*

ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd MeanCurv
GausCurv FoldInd CurvInd

Thusly, I am not confident that any of these values represent the lgi value.

Can someone confirm that the correct value would appear under the thickness
column in this case?

Thank you

Kate
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[Freesurfer] local gyrification index (lGI) Error in Design

[Katherine Damme]

Hello FreeSurfer Group

I would like to make a two group comparison controlling for both gender and
medication status. The only way that I have sorted out doing this is to
make eight groups (ClinicalGroup x Sex x Meds) but I get an error that my
design is poorly scaled:

 

ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08



Possible problem with experimental design:

Check for duplicate entries and/or lack of range of

continuous variables within a class.

If you seek help with this problem, make sure to send:

  1. Your command line:

mri_glmfit --y lh.lgi.mgh --fsgd FSGD_GroupSexTP_AntiPsych.txt --glmdir
lh.lgi.glmdir --surf average lh --C contrast.txt

  2. The FSGD file (if using one)

  3. And the design matrix above
GroupDescriptorFile 1
Title GroupGenderAntipsychotic
Class UHR_F_1
Class UHR_F_2
Class UHR_M_1
Class UHR_M_2
Class HC_F_1
Class HC_F_2
Class HC_M_1
Class HC_M_2
Variables Antipsychotic
Input 1001_MR1 UHR_F_1 0
Input 1001_MR2 UHR_F_2 0
Input 1004_MR1 UHR_F_1 0
Input 1004_MR3 UHR_F_2 0
Input 1005_MR1 UHR_M_1 1
Input 1005_MR2 UHR_M_2 1
Input 1006_MR1 UHR_F_1 1
Input 1006_MR2 UHR_F_2 1
Input 1007_MR1 UHR_M_1 0
Input 1007_MR3 UHR_M_2 0
Input 1008_MR1 UHR_F_1 0
Input 1008_MR2 UHR_F_2 0
Input 1009_MR1 UHR_M_1 0
Input 1009_MR2 UHR_M_2 0
Input 1010_MR1 UHR_M_1 0
Input 1010_MR2 UHR_M_2 0
Input 1011_MR1 UHR_M_1 0
Input 1011_MR2 UHR_M_2 0
Input 1012_MR1 UHR_M_1 1
Input 1012_MR2 UHR_M_2 1
Input 1014_MR1 UHR_F_1 0
Input 1014_MR2 UHR_F_2 0
Input 1016_MR1 UHR_M_1 0
Input 1016_MR2 UHR_M_2 0
Input 1017_MR1 UHR_F_1 0
Input 1017_MR2 UHR_F_2 0
Input 1018_MR1 UHR_M_1 0
Input 1018_MR2 UHR_M_2 0
Input 1020_MR1 UHR_F_1 0
Input 1020_MR2 UHR_F_2 0
Input 1021_MR1 UHR_F_1 0
Input 1021_MR2 UHR_F_2 0
Input 1023_MR1 UHR_M_1 0
Input 1023_MR2 UHR_M_2 0
Input 1024_MR1 UHR_M_1 1
Input 1024_MR2 UHR_M_2 1
Input 1025_MR1 UHR_M_1 0
Input 1025_MR2 UHR_M_2 0
Input 1027_MR1 UHR_M_1 0
Input 1027_MR2 UHR_M_2 0
Input 1029_MR1 UHR_M_1 0
Input 1029_MR2 UHR_M_2 0
Input 1031_MR1 UHR_M_1 0
Input 1031_MR2 UHR_M_2 0
Input 1032_MR1 UHR_M_1 0
Input 1032_MR2 UHR_M_2 0
Input 1033_MR1 UHR_M_1 0
Input 1033_MR2 UHR_M_2 0
Input 1034_MR1 UHR_F_1 0
Input 1034_MR2 UHR_F_2 0
Input 1035_MR1 UHR_M_1 0
Input 1035_MR2 UHR_M_2 0
Input 1036_MR1 UHR_F_1 0
Input 1036_MR2 UHR_F_2 0
Input 1037_MR1 UHR_M_1 0
Input 1037_MR2 UHR_M_2 0
Input 1039_MR1 UHR_M_1 0
Input 1039_MR2 UHR_M_2 0
Input 1040_MR1 UHR_F_1 0
Input 1040_MR2 UHR_F_2 0
Input 1043_MR1 UHR_M_1 1
Input 1043_MR2 UHR_M_2 1
Input 1046_MR1 UHR_F_1 0
Input 1046_MR2 UHR_F_2 0
Input 1050_MR1 UHR_F_1 0
Input 1050_MR2 UHR_F_2 0
Input 1053_MR1 UHR_M_1 0
Input 1053_MR2 UHR_M_2 0
Input 1054_MR1 UHR_F_1 0
Input 1054_MR2 UHR_F_2 0
Input 1058_MR1 UHR_M_1 0
Input 1058_MR2 UHR_M_2 0
Input 2001_MR1 HC_M_1 0
Input 2001_MR2 HC_M_2 0
Input 2004_MR1 HC_F_1 0
Input 2004_MR2 HC_F_2 0
Input 2007_MR1 HC_M_1 0
Input 2007_MR2 HC_M_2 0
Input 2010_MR1 HC_M_1 0
Input 2010_MR2 HC_M_2 0
Input 2011_MR1 HC_F_1 0
Input 2011_MR2 HC_F_2 0
Input 2012_MR1 HC_F_1 0
Input 2012_MR2 HC_F_2 0
Input 2013_MR1 HC_F_1 0
Input 2013_MR2 HC_F_2 0
Input 2015_MR1 HC_F_1 0
Input 2015_MR2 HC_F_2 0
Input 2016_MR1 HC_F_1 0
Input 2016_MR2 HC_F_2 0
Input 2017_MR1 HC_F_1 0
Input 2017_MR2 HC_F_2 0
Input 2018_MR1 HC_F_1 0
Input 2018_MR2 HC_F_2 0
Input 2019_MR1 HC_M_1 0
Input 2019_MR2 HC_M_2 0
Input 2024_MR1 HC_F_1 0
Input 2024_MR2 HC_F_2 0
Input 2025_MR1 HC_M_1 0
Input 2025_MR2 HC_M_2 0
Input 2027_MR1 HC_F_1 0
Input 2027_MR2 HC_F_2 0
Input 2029_MR1 HC_M_1 0
Input 2029_MR2 HC_M_2 0
Input 2030_MR1 HC_F_1 0
Input 2030_MR2 HC_F_2 0
Input 2031_MR1 HC_F_1 0
Input 2031_MR2 HC_F_2 0
Input 2032_MR1 HC_M_1 0
Input 2032_MR2 HC_M_2 0
Input 2033_MR1 HC_F_1 0
Input 2033_MR2 HC_F_2 0
Input 2034_MR1 HC_F_1 0
Input 2034_MR2 HC_F_2 0
Input 2038_MR1 HC_F_1 0
Input 2038_MR2 HC_F_2 0
Input 2041_MR1 HC_F_1 0
Input 2041_MR2 HC_F_2 0
Input 2042_MR1 HC_M_1 0
Input 2042_MR2 HC_M_2 0
Input 2043_MR1 HC_F_1 0
Input 2043_MR2 HC_F_2 0
Input 2050_MR1 HC_F_1 0
Input 2050_MR2 HC_F_2 0
Input 2053_MR1 HC_M_1 0
Input 2053_MR2 HC_M_2 0
Input 2057_MR1 HC_F_1 0
Input 2057_MR2 HC_F_2 0
Input 2058_MR1 HC_M_1 0
Input 2058_MR2 HC_M_2 0
Input 2059_MR1 HC_M_1 0
Input 2059_MR2 HC_M_2 0
Input 2061_MR1 HC_F_1 0
Input 2061_MR2 HC_F_2 0
Input 1048_MR1 UHR_M_1 1
Input 1048_MR2 UHR_M_2 1
Input 1061_MR1 UHR_M_1 1
Input 1061_MR2 UHR_M_2 1
Input 1062_MR1 UHR_M_1 0
Input 1062_MR2 UHR_M_2 0
Input 1067_MR1 UHR_M_1 0
Input 1067_MR2 UHR_M_2 0
Input 1074_MR1 UHR_F_1 0
Input 1074_MR2 UHR_F_2 0
Input 1075_MR1 UHR_F_1 0
Input 1075_MR2 UHR_F_2 0
Input 2062_MR1 HC_M_1 0
Input 2062_MR2 HC_M_2 0
Input 2065_MR1 HC_F_1 0
Input 2065_MR2 HC_F_2 0
Input 2067_MR1 HC_F_1 0
Input 2067_MR2 HC_F_2 0
Input 2070_MR1 HC_F_1 0
Input 2070_MR2 HC_F_2 0
Input 2071_MR1 HC_M_1 0
Input 2071_MR2 HC_M_2 0
Input 2076_MR1 HC_F_1 0
Input 2076_MR2 HC_F_2 0
Input 2078_MR1 HC_F_1 0
Input 2078_MR2 HC_F_2 0


command_matrix
Description: Binary data

Re: [Freesurfer] Extracting significant clusters after qdec analyses

[Katherine Damme]

Thanks Douglas. I am not sure that I understand. Will you please review the
commands below?

I believe I need to complete something like:

mri_surfcluster --in ${qdecoutputfolder}/cache.th40.abs.sig.masked.mgh
--fdr 0.05 --mask ${qdecoutputfolder}/mask.mgh --csd
/usr/local/freesurfer/average/mult-comp-cor/rh/cortex/fwhm25/abs/th40/mc-z.csd
--surf pial --ocn ${qdecoutputfolder}/

Which puts out a *.w file, a COR-00#, and COR.info, but I am not sure which
file I should supply to -- seg

mri_segstats --seg ??  --i y.mgh --avgfw ${nameoftextoutput}  --exludeid 0

Could I supply the ocn file from the mri_glmfit-sim?


On Mon, Jan 23, 2017 at 7:10 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote:

> It is probably better to work with the y.mgh file that qdec produces. It
> is in fsaverage space. If you create an ocn file with mri_surfcluster, you
> can feed that as the --seg to mri_segstats (along with --i y.mgh), spec the
> output with --avgwf to get a matrix of nsubjects  by nclusters (make sure
> to also include --exludeid 0)
>
>
> On 01/23/2017 08:00 PM, Katherine Damme wrote:
>
>> Thank you so much!
>>
>> This got me to the stage of having separate labels for each significant
>> cluster, but I would like to extract the values from each subject to look
>> at the raw data.
>>
>> Do I have to use mri_label2label to move the label into each individual's
>> space?
>>
>> Can I use aparcstats2table to get a table of the individual values of the
>> label?
>> (It seems that this is set up for the segmentation data)
>>
>> Thank you again!
>>
>>
>> On Mon, Jan 23, 2017 at 11:44 AM, Douglas N Greve <
>> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>
>> Try mri_surfcluster. Run it with --help to get usage. You can set the
>>     threshold with --fdr. Make sure to use the --mask option passing
>> it the
>> mask.mgh from the qdec  output
>>
>>
>> On 01/22/2017 07:56 PM, Katherine Damme wrote:
>> > Hello Everyone,
>> >
>> > Is there a way to extract the significant clusters as masks from
>> > significant group comparisons using qdec?
>> >
>> > All I can seem to find is  mri_glmfit-sim which doesn't quite
>> > replicate the QDEC FDR 0.05 output and doesn't seem to make anything
>> > that I could extract as a label, or hand drawing an ROI.
>> >
>> > I am working with a longitudinal model of cortical thickness, and
>> > would like to extract the average thickness of each significant
>> > cluster to understand the change in thickness.
>> >
>> > Thank you.
>> >
>> > Kate Damme
>> >
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
>> Phone Number: 617-724-2358 
>> Fax: 617-726-7422 
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> <https://gate.nmr.mgh.harvard.edu/filedrop2>
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>> Outgoing:
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
>>
>> ___
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>> >
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> <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
>> <htt

[Freesurfer] Extracting significant clusters after qdec analyses

[Katherine Damme]

Hello Everyone,

Is there a way to extract the significant clusters as masks from
significant group comparisons using qdec?

All I can seem to find is  mri_glmfit-sim which doesn't quite replicate the
QDEC FDR 0.05 output and doesn't seem to make anything that I could extract
as a label, or hand drawing an ROI.

I am working with a longitudinal model of cortical thickness, and would
like to extract the average thickness of each significant cluster to
understand the change in thickness.

Thank you.

Kate Damme
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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
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Re: [Freesurfer] Tracula Set: No Match

[Katherine Damme]

Is it possible to run tracula with out a phase mapping MRI scan? All I have
in this data is a MPRAGE and DWI images weighted at either 0 or 1000.

Thank you.

On Tue, Jan 3, 2017 at 1:07 PM, Yendiki, Anastasia <ayend...@mgh.harvard.edu
> wrote:

> Hi Katherine - You need to have an appropriate field mapping MRI scan.
>
> Best,
> a.y
>
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine Damme [
> katherine.da...@gmail.com]
> *Sent:* Sunday, January 01, 2017 5:16 PM
>
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Tracula Set: No Match
>
> Sorry the phase map. How do I generate an appropriately formatted phase
> map?
>
> On Sun, Jan 1, 2017 at 4:15 PM, Katherine Damme <katherine.da...@gmail.com
> > wrote:
>
>> How do I generate a field map?
>>
>> On Mon, Dec 19, 2016 at 10:09 PM, Yendiki, Anastasia <
>> ayend...@mgh.harvard.edu> wrote:
>>
>>> No - there is no relation between B0 field inhomogeneities (measured by
>>> a field map) and b=0 volumes. The capital B refers to the magnetic field in
>>> the scanner, the small b is the b-value (diffusion weighting).
>>>
>>> ------
>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
>>> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine Damme [
>>> katherine.da...@gmail.com]
>>> *Sent:* Monday, December 19, 2016 11:01 PM
>>>
>>> *To:* Freesurfer support list
>>> *Subject:* Re: [Freesurfer] Tracula Set: No Match
>>>
>>> Is this meant to be calculated from the B0 dicoms?
>>>
>>> On Mon, Dec 19, 2016 at 12:44 PM, Yendiki, Anastasia <
>>> ayend...@mgh.harvard.edu> wrote:
>>>
>>>> No, it's a separate scan that you provide.
>>>>
>>>> --
>>>> *From:* Katherine Damme [katherine.da...@gmail.com]
>>>> *Sent:* Monday, December 19, 2016 1:43 PM
>>>>
>>>> *To:* Freesurfer support list; Anastasia Yendiki
>>>> *Subject:* Re: [Freesurfer] Tracula Set: No Match
>>>>
>>>> This is being generated by an earlier step in the trac-all -prep right?
>>>>
>>>> On Fri, Dec 16, 2016 at 4:23 PM, Yendiki, Anastasia <
>>>> ayend...@mgh.harvard.edu> wrote:
>>>>
>>>>> It doesn't recognize the format of your field map. It assumes that the
>>>>> field map has either 2 frames (2 phase maps) or 1 frame (a phase 
>>>>> difference
>>>>> map).
>>>>>
>>>>> --
>>>>> *From:* Katherine Damme [katherine.da...@gmail.com]
>>>>> *Sent:* Friday, December 16, 2016 5:18 PM
>>>>> *To:* Freesurfer support list; Anastasia Yendiki
>>>>> *Subject:* Re: [Freesurfer] Tracula Set: No Match
>>>>>
>>>>> When I run this on the command line it seems to be completing the
>>>>> fslroi step fine:
>>>>>
>>>>> "fslroi 
>>>>> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_eddy.nii.gz
>>>>> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/lowb.nii.gz 0 1
>>>>> ERROR: Unrecognized format of phase map /media/Data/Temple/Temple_Trac
>>>>> ula/31313422_10128/dmri/b0pha.nii.gz
>>>>> Linux katelinux.psych.northwestern.edu 2.6.32-642.6.2.el6.x86_64 #1
>>>>> SMP Mon Oct 24 10:22:33 EDT 2016 x86_64 x86_64 x86_64 GNU/Linux
>>>>>
>>>>> trac-preproc exited with ERRORS at Fri Dec 16 15:38:48 CST 2016
>>>>>
>>>>> [ksd770@katelinux Temple_Tracula]# fslroi
>>>>> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_eddy.nii.gz
>>>>> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/lowb.nii.gz 0 1
>>>>> [ksd770@katelinux Temple_Tracula]# trac-all -prep -c dmrirc_10128.txt"
>>>>>
>>>>> What is the next step in the code where it is failing?
>>>>>
>>>>> On Wed, Dec 14, 2016 at 9:19 PM, Katherine Damme <
>>>>> katherine.da...@gmail.com> wrote:
>>>>>
>>>>>> I am now getting this error. I am not sure if this is a new issue or
>>>>>> related.
>>>>>>
>>>>>> fslorient -forceradiological /media/Data/Temple/Temple_Trac
>>>>>> ula/31313422_10128/dmri/b0pha.nii.gz
>>>>>>
>&

Re: [Freesurfer] Tracula Set: No Match

[Katherine Damme]

Sorry the phase map. How do I generate an appropriately formatted phase map?

On Sun, Jan 1, 2017 at 4:15 PM, Katherine Damme <katherine.da...@gmail.com>
wrote:

> How do I generate a field map?
>
> On Mon, Dec 19, 2016 at 10:09 PM, Yendiki, Anastasia <
> ayend...@mgh.harvard.edu> wrote:
>
>> No - there is no relation between B0 field inhomogeneities (measured by a
>> field map) and b=0 volumes. The capital B refers to the magnetic field in
>> the scanner, the small b is the b-value (diffusion weighting).
>>
>> --
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
>> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine Damme [
>> katherine.da...@gmail.com]
>> *Sent:* Monday, December 19, 2016 11:01 PM
>>
>> *To:* Freesurfer support list
>> *Subject:* Re: [Freesurfer] Tracula Set: No Match
>>
>> Is this meant to be calculated from the B0 dicoms?
>>
>> On Mon, Dec 19, 2016 at 12:44 PM, Yendiki, Anastasia <
>> ayend...@mgh.harvard.edu> wrote:
>>
>>> No, it's a separate scan that you provide.
>>>
>>> --
>>> *From:* Katherine Damme [katherine.da...@gmail.com]
>>> *Sent:* Monday, December 19, 2016 1:43 PM
>>>
>>> *To:* Freesurfer support list; Anastasia Yendiki
>>> *Subject:* Re: [Freesurfer] Tracula Set: No Match
>>>
>>> This is being generated by an earlier step in the trac-all -prep right?
>>>
>>> On Fri, Dec 16, 2016 at 4:23 PM, Yendiki, Anastasia <
>>> ayend...@mgh.harvard.edu> wrote:
>>>
>>>> It doesn't recognize the format of your field map. It assumes that the
>>>> field map has either 2 frames (2 phase maps) or 1 frame (a phase difference
>>>> map).
>>>>
>>>> --
>>>> *From:* Katherine Damme [katherine.da...@gmail.com]
>>>> *Sent:* Friday, December 16, 2016 5:18 PM
>>>> *To:* Freesurfer support list; Anastasia Yendiki
>>>> *Subject:* Re: [Freesurfer] Tracula Set: No Match
>>>>
>>>> When I run this on the command line it seems to be completing the
>>>> fslroi step fine:
>>>>
>>>> "fslroi 
>>>> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_eddy.nii.gz
>>>> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/lowb.nii.gz 0 1
>>>> ERROR: Unrecognized format of phase map /media/Data/Temple/Temple_Trac
>>>> ula/31313422_10128/dmri/b0pha.nii.gz
>>>> Linux katelinux.psych.northwestern.edu 2.6.32-642.6.2.el6.x86_64 #1
>>>> SMP Mon Oct 24 10:22:33 EDT 2016 x86_64 x86_64 x86_64 GNU/Linux
>>>>
>>>> trac-preproc exited with ERRORS at Fri Dec 16 15:38:48 CST 2016
>>>>
>>>> [ksd770@katelinux Temple_Tracula]# fslroi
>>>> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_eddy.nii.gz
>>>> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/lowb.nii.gz 0 1
>>>> [ksd770@katelinux Temple_Tracula]# trac-all -prep -c dmrirc_10128.txt"
>>>>
>>>> What is the next step in the code where it is failing?
>>>>
>>>> On Wed, Dec 14, 2016 at 9:19 PM, Katherine Damme <
>>>> katherine.da...@gmail.com> wrote:
>>>>
>>>>> I am now getting this error. I am not sure if this is a new issue or
>>>>> related.
>>>>>
>>>>> fslorient -forceradiological /media/Data/Temple/Temple_Trac
>>>>> ula/31313422_10128/dmri/b0pha.nii.gz
>>>>>
>>>>> mri_probedicom --i //media/Data/Temple/Temple_Tra
>>>>> cula/31313422_10128/dti_dicom/31313422_10128.MR.Temple.9.1.20140806.182244.xfrp16.dcm
>>>>> > /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/b0info.dat
>>>>>
>>>>> TE: Subscript out of range.
>>>>>
>>>>> fslroi 
>>>>> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_eddy.nii.gz
>>>>> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/lowb.nii.gz 0 1
>>>>>
>>>>> ERROR: Unrecognized format of phase map /media/Data/Temple/Temple_Trac
>>>>> ula/31313422_10128/dmri/b0pha.nii.gz
>>>>>
>>>>> Linux katelinux.psych.northwestern.edu 2.6.32-642.6.2.el6.x86_64 #1
>>>>> SMP Mon Oct 24 10:22:33 EDT 2016 x86_64 x86_64 x86_64 GNU/Linux
>>>>>
>>>>> I check all of these images and I can open them.
>>>>>
>&

Re: [Freesurfer] Tracula Set: No Match

[Katherine Damme]

How do I generate a field map?

On Mon, Dec 19, 2016 at 10:09 PM, Yendiki, Anastasia <
ayend...@mgh.harvard.edu> wrote:

> No - there is no relation between B0 field inhomogeneities (measured by a
> field map) and b=0 volumes. The capital B refers to the magnetic field in
> the scanner, the small b is the b-value (diffusion weighting).
>
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine Damme [
> katherine.da...@gmail.com]
> *Sent:* Monday, December 19, 2016 11:01 PM
>
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Tracula Set: No Match
>
> Is this meant to be calculated from the B0 dicoms?
>
> On Mon, Dec 19, 2016 at 12:44 PM, Yendiki, Anastasia <
> ayend...@mgh.harvard.edu> wrote:
>
>> No, it's a separate scan that you provide.
>>
>> --
>> *From:* Katherine Damme [katherine.da...@gmail.com]
>> *Sent:* Monday, December 19, 2016 1:43 PM
>>
>> *To:* Freesurfer support list; Anastasia Yendiki
>> *Subject:* Re: [Freesurfer] Tracula Set: No Match
>>
>> This is being generated by an earlier step in the trac-all -prep right?
>>
>> On Fri, Dec 16, 2016 at 4:23 PM, Yendiki, Anastasia <
>> ayend...@mgh.harvard.edu> wrote:
>>
>>> It doesn't recognize the format of your field map. It assumes that the
>>> field map has either 2 frames (2 phase maps) or 1 frame (a phase difference
>>> map).
>>>
>>> --
>>> *From:* Katherine Damme [katherine.da...@gmail.com]
>>> *Sent:* Friday, December 16, 2016 5:18 PM
>>> *To:* Freesurfer support list; Anastasia Yendiki
>>> *Subject:* Re: [Freesurfer] Tracula Set: No Match
>>>
>>> When I run this on the command line it seems to be completing the fslroi
>>> step fine:
>>>
>>> "fslroi 
>>> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_eddy.nii.gz
>>> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/lowb.nii.gz 0 1
>>> ERROR: Unrecognized format of phase map /media/Data/Temple/Temple_Trac
>>> ula/31313422_10128/dmri/b0pha.nii.gz
>>> Linux katelinux.psych.northwestern.edu 2.6.32-642.6.2.el6.x86_64 #1 SMP
>>> Mon Oct 24 10:22:33 EDT 2016 x86_64 x86_64 x86_64 GNU/Linux
>>>
>>> trac-preproc exited with ERRORS at Fri Dec 16 15:38:48 CST 2016
>>>
>>> [ksd770@katelinux Temple_Tracula]# fslroi /media/Data/Temple/Temple_Trac
>>> ula/31313422_10128/dmri/dwi_eddy.nii.gz /media/Data/Temple/Temple_Trac
>>> ula/31313422_10128/dmri/lowb.nii.gz 0 1
>>> [ksd770@katelinux Temple_Tracula]# trac-all -prep -c dmrirc_10128.txt"
>>>
>>> What is the next step in the code where it is failing?
>>>
>>> On Wed, Dec 14, 2016 at 9:19 PM, Katherine Damme <
>>> katherine.da...@gmail.com> wrote:
>>>
>>>> I am now getting this error. I am not sure if this is a new issue or
>>>> related.
>>>>
>>>> fslorient -forceradiological /media/Data/Temple/Temple_Trac
>>>> ula/31313422_10128/dmri/b0pha.nii.gz
>>>>
>>>> mri_probedicom --i //media/Data/Temple/Temple_Tra
>>>> cula/31313422_10128/dti_dicom/31313422_10128.MR.Temple.9.1.20140806.182244.xfrp16.dcm
>>>> > /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/b0info.dat
>>>>
>>>> TE: Subscript out of range.
>>>>
>>>> fslroi 
>>>> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_eddy.nii.gz
>>>> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/lowb.nii.gz 0 1
>>>>
>>>> ERROR: Unrecognized format of phase map /media/Data/Temple/Temple_Trac
>>>> ula/31313422_10128/dmri/b0pha.nii.gz
>>>>
>>>> Linux katelinux.psych.northwestern.edu 2.6.32-642.6.2.el6.x86_64 #1
>>>> SMP Mon Oct 24 10:22:33 EDT 2016 x86_64 x86_64 x86_64 GNU/Linux
>>>>
>>>> I check all of these images and I can open them.
>>>>
>>>> On Tue, Dec 13, 2016 at 7:59 PM, Yendiki, Anastasia <
>>>> ayend...@mgh.harvard.edu> wrote:
>>>>
>>>>> Hi Katherine - Can you please use the attached version and tell me if
>>>>> it works? You'll have to copy it into $FREESURFER_HOME/bin, to overwrite
>>>>> the version of xfmrot that you have now. If it works, we'll include it in
>>>>> the next version. Thanks!
>>>>>
>>>>> a.y
>>>&

Re: [Freesurfer] Tracula Set: No Match

[Katherine Damme]

Is this meant to be calculated from the B0 dicoms?

On Mon, Dec 19, 2016 at 12:44 PM, Yendiki, Anastasia <
ayend...@mgh.harvard.edu> wrote:

> No, it's a separate scan that you provide.
>
> --
> *From:* Katherine Damme [katherine.da...@gmail.com]
> *Sent:* Monday, December 19, 2016 1:43 PM
>
> *To:* Freesurfer support list; Anastasia Yendiki
> *Subject:* Re: [Freesurfer] Tracula Set: No Match
>
> This is being generated by an earlier step in the trac-all -prep right?
>
> On Fri, Dec 16, 2016 at 4:23 PM, Yendiki, Anastasia <
> ayend...@mgh.harvard.edu> wrote:
>
>> It doesn't recognize the format of your field map. It assumes that the
>> field map has either 2 frames (2 phase maps) or 1 frame (a phase difference
>> map).
>>
>> --
>> *From:* Katherine Damme [katherine.da...@gmail.com]
>> *Sent:* Friday, December 16, 2016 5:18 PM
>> *To:* Freesurfer support list; Anastasia Yendiki
>> *Subject:* Re: [Freesurfer] Tracula Set: No Match
>>
>> When I run this on the command line it seems to be completing the fslroi
>> step fine:
>>
>> "fslroi /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_eddy.nii.gz
>> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/lowb.nii.gz 0 1
>> ERROR: Unrecognized format of phase map /media/Data/Temple/Temple_Trac
>> ula/31313422_10128/dmri/b0pha.nii.gz
>> Linux katelinux.psych.northwestern.edu 2.6.32-642.6.2.el6.x86_64 #1 SMP
>> Mon Oct 24 10:22:33 EDT 2016 x86_64 x86_64 x86_64 GNU/Linux
>>
>> trac-preproc exited with ERRORS at Fri Dec 16 15:38:48 CST 2016
>>
>> [ksd770@katelinux Temple_Tracula]# fslroi /media/Data/Temple/Temple_Trac
>> ula/31313422_10128/dmri/dwi_eddy.nii.gz /media/Data/Temple/Temple_Trac
>> ula/31313422_10128/dmri/lowb.nii.gz 0 1
>> [ksd770@katelinux Temple_Tracula]# trac-all -prep -c dmrirc_10128.txt"
>>
>> What is the next step in the code where it is failing?
>>
>> On Wed, Dec 14, 2016 at 9:19 PM, Katherine Damme <
>> katherine.da...@gmail.com> wrote:
>>
>>> I am now getting this error. I am not sure if this is a new issue or
>>> related.
>>>
>>> fslorient -forceradiological /media/Data/Temple/Temple_Trac
>>> ula/31313422_10128/dmri/b0pha.nii.gz
>>>
>>> mri_probedicom --i //media/Data/Temple/Temple_Tra
>>> cula/31313422_10128/dti_dicom/31313422_10128.MR.Temple.9.1.20140806.182244.xfrp16.dcm
>>> > /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/b0info.dat
>>>
>>> TE: Subscript out of range.
>>>
>>> fslroi /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_eddy.nii.gz
>>> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/lowb.nii.gz 0 1
>>>
>>> ERROR: Unrecognized format of phase map /media/Data/Temple/Temple_Trac
>>> ula/31313422_10128/dmri/b0pha.nii.gz
>>>
>>> Linux katelinux.psych.northwestern.edu 2.6.32-642.6.2.el6.x86_64 #1 SMP
>>> Mon Oct 24 10:22:33 EDT 2016 x86_64 x86_64 x86_64 GNU/Linux
>>>
>>> I check all of these images and I can open them.
>>>
>>> On Tue, Dec 13, 2016 at 7:59 PM, Yendiki, Anastasia <
>>> ayend...@mgh.harvard.edu> wrote:
>>>
>>>> Hi Katherine - Can you please use the attached version and tell me if
>>>> it works? You'll have to copy it into $FREESURFER_HOME/bin, to overwrite
>>>> the version of xfmrot that you have now. If it works, we'll include it in
>>>> the next version. Thanks!
>>>>
>>>> a.y
>>>>
>>>> --
>>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
>>>> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine Damme [
>>>> katherine.da...@gmail.com]
>>>> *Sent:* Tuesday, December 13, 2016 9:38 AM
>>>>
>>>> *To:* Freesurfer support list
>>>> *Subject:* Re: [Freesurfer] Tracula Set: No Match
>>>>
>>>>
>>>>
>>>> On Tue, Dec 13, 2016 at 8:34 AM, Yendiki, Anastasia <
>>>> ayend...@mgh.harvard.edu> wrote:
>>>>
>>>>> Ok, if you also send me the first file, /media/Data/Temple/Temple_Trac
>>>>> ula/31313422_10128/dmri/dwi.ecclog, I'll see if I can replicate the
>>>>> error.
>>>>>
>>>>> --
>>>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
>>>>> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine Damme

Re: [Freesurfer] Tracula Set: No Match

[Katherine Damme]

This is being generated by an earlier step in the trac-all -prep right?

On Fri, Dec 16, 2016 at 4:23 PM, Yendiki, Anastasia <
ayend...@mgh.harvard.edu> wrote:

> It doesn't recognize the format of your field map. It assumes that the
> field map has either 2 frames (2 phase maps) or 1 frame (a phase difference
> map).
>
> --
> *From:* Katherine Damme [katherine.da...@gmail.com]
> *Sent:* Friday, December 16, 2016 5:18 PM
> *To:* Freesurfer support list; Anastasia Yendiki
> *Subject:* Re: [Freesurfer] Tracula Set: No Match
>
> When I run this on the command line it seems to be completing the fslroi
> step fine:
>
> "fslroi /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_eddy.nii.gz
> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/lowb.nii.gz 0 1
> ERROR: Unrecognized format of phase map /media/Data/Temple/Temple_
> Tracula/31313422_10128/dmri/b0pha.nii.gz
> Linux katelinux.psych.northwestern.edu 2.6.32-642.6.2.el6.x86_64 #1 SMP
> Mon Oct 24 10:22:33 EDT 2016 x86_64 x86_64 x86_64 GNU/Linux
>
> trac-preproc exited with ERRORS at Fri Dec 16 15:38:48 CST 2016
>
> [ksd770@katelinux Temple_Tracula]# fslroi /media/Data/Temple/Temple_
> Tracula/31313422_10128/dmri/dwi_eddy.nii.gz /media/Data/Temple/Temple_
> Tracula/31313422_10128/dmri/lowb.nii.gz 0 1
> [ksd770@katelinux Temple_Tracula]# trac-all -prep -c dmrirc_10128.txt"
>
> What is the next step in the code where it is failing?
>
> On Wed, Dec 14, 2016 at 9:19 PM, Katherine Damme <
> katherine.da...@gmail.com> wrote:
>
>> I am now getting this error. I am not sure if this is a new issue or
>> related.
>>
>> fslorient -forceradiological /media/Data/Temple/Temple_Trac
>> ula/31313422_10128/dmri/b0pha.nii.gz
>>
>> mri_probedicom --i //media/Data/Temple/Temple_Tra
>> cula/31313422_10128/dti_dicom/31313422_10128.MR.Temple.9.1.20140806.182244.xfrp16.dcm
>> > /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/b0info.dat
>>
>> TE: Subscript out of range.
>>
>> fslroi /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_eddy.nii.gz
>> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/lowb.nii.gz 0 1
>>
>> ERROR: Unrecognized format of phase map /media/Data/Temple/Temple_Trac
>> ula/31313422_10128/dmri/b0pha.nii.gz
>>
>> Linux katelinux.psych.northwestern.edu 2.6.32-642.6.2.el6.x86_64 #1 SMP
>> Mon Oct 24 10:22:33 EDT 2016 x86_64 x86_64 x86_64 GNU/Linux
>>
>> I check all of these images and I can open them.
>>
>> On Tue, Dec 13, 2016 at 7:59 PM, Yendiki, Anastasia <
>> ayend...@mgh.harvard.edu> wrote:
>>
>>> Hi Katherine - Can you please use the attached version and tell me if it
>>> works? You'll have to copy it into $FREESURFER_HOME/bin, to overwrite the
>>> version of xfmrot that you have now. If it works, we'll include it in the
>>> next version. Thanks!
>>>
>>> a.y
>>>
>>> --
>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
>>> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine Damme [
>>> katherine.da...@gmail.com]
>>> *Sent:* Tuesday, December 13, 2016 9:38 AM
>>>
>>> *To:* Freesurfer support list
>>> *Subject:* Re: [Freesurfer] Tracula Set: No Match
>>>
>>>
>>>
>>> On Tue, Dec 13, 2016 at 8:34 AM, Yendiki, Anastasia <
>>> ayend...@mgh.harvard.edu> wrote:
>>>
>>>> Ok, if you also send me the first file, /media/Data/Temple/Temple_Trac
>>>> ula/31313422_10128/dmri/dwi.ecclog, I'll see if I can replicate the
>>>> error.
>>>>
>>>> --
>>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
>>>> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine Damme [
>>>> katherine.da...@gmail.com]
>>>> *Sent:* Tuesday, December 13, 2016 9:21 AM
>>>>
>>>> *To:* Freesurfer support list
>>>> *Subject:* Re: [Freesurfer] Tracula Set: No Match
>>>>
>>>> Yes. I immediately tried to enter the command in manually, checked the
>>>> paths, and looked at the command manual for any format errors.
>>>>
>>>> [ksd770@katelinux Temple_Tracula]$ xfmrot
>>>> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.ecclog
>>>> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs.norot
>>>> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs
>>>>
>>>> set: No match.
>>>>
>>>> On Wed, Dec 7, 2016 at

Re: [Freesurfer] Tracula Set: No Match

[Katherine Damme]

When I run this on the command line it seems to be completing the fslroi
step fine:

"fslroi
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_eddy.nii.gz
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/lowb.nii.gz 0 1
ERROR: Unrecognized format of phase map
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/b0pha.nii.gz
Linux katelinux.psych.northwestern.edu 2.6.32-642.6.2.el6.x86_64 #1 SMP Mon
Oct 24 10:22:33 EDT 2016 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Fri Dec 16 15:38:48 CST 2016

[ksd770@katelinux Temple_Tracula]# fslroi
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_eddy.nii.gz
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/lowb.nii.gz 0 1
[ksd770@katelinux Temple_Tracula]# trac-all -prep -c dmrirc_10128.txt"

What is the next step in the code where it is failing?

On Wed, Dec 14, 2016 at 9:19 PM, Katherine Damme <katherine.da...@gmail.com>
wrote:

> I am now getting this error. I am not sure if this is a new issue or
> related.
>
> fslorient -forceradiological /media/Data/Temple/Temple_
> Tracula/31313422_10128/dmri/b0pha.nii.gz
>
> mri_probedicom --i //media/Data/Temple/Temple_Tracula/31313422_10128/dti_
> dicom/31313422_10128.MR.Temple.9.1.20140806.182244.xfrp16.dcm >
> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/b0info.dat
>
> TE: Subscript out of range.
>
> fslroi /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_eddy.nii.gz
> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/lowb.nii.gz 0 1
>
> ERROR: Unrecognized format of phase map /media/Data/Temple/Temple_
> Tracula/31313422_10128/dmri/b0pha.nii.gz
>
> Linux katelinux.psych.northwestern.edu 2.6.32-642.6.2.el6.x86_64 #1 SMP
> Mon Oct 24 10:22:33 EDT 2016 x86_64 x86_64 x86_64 GNU/Linux
>
> I check all of these images and I can open them.
>
> On Tue, Dec 13, 2016 at 7:59 PM, Yendiki, Anastasia <
> ayend...@mgh.harvard.edu> wrote:
>
>> Hi Katherine - Can you please use the attached version and tell me if it
>> works? You'll have to copy it into $FREESURFER_HOME/bin, to overwrite the
>> version of xfmrot that you have now. If it works, we'll include it in the
>> next version. Thanks!
>>
>> a.y
>>
>> ------
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
>> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine Damme [
>> katherine.da...@gmail.com]
>> *Sent:* Tuesday, December 13, 2016 9:38 AM
>>
>> *To:* Freesurfer support list
>> *Subject:* Re: [Freesurfer] Tracula Set: No Match
>>
>>
>>
>> On Tue, Dec 13, 2016 at 8:34 AM, Yendiki, Anastasia <
>> ayend...@mgh.harvard.edu> wrote:
>>
>>> Ok, if you also send me the first file, /media/Data/Temple/Temple_Trac
>>> ula/31313422_10128/dmri/dwi.ecclog, I'll see if I can replicate the
>>> error.
>>>
>>> --
>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
>>> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine Damme [
>>> katherine.da...@gmail.com]
>>> *Sent:* Tuesday, December 13, 2016 9:21 AM
>>>
>>> *To:* Freesurfer support list
>>> *Subject:* Re: [Freesurfer] Tracula Set: No Match
>>>
>>> Yes. I immediately tried to enter the command in manually, checked the
>>> paths, and looked at the command manual for any format errors.
>>>
>>> [ksd770@katelinux Temple_Tracula]$ xfmrot /media/Data/Temple/Temple_Trac
>>> ula/31313422_10128/dmri/dwi.ecclog /media/Data/Temple/Temple_Trac
>>> ula/31313422_10128/dmri/bvecs.norot /media/Data/Temple/Temple_Trac
>>> ula/31313422_10128/dmri/bvecs
>>>
>>> set: No match.
>>>
>>> On Wed, Dec 7, 2016 at 2:41 PM, Yendiki, Anastasia <
>>> ayend...@mgh.harvard.edu> wrote:
>>>
>>>> Thanks. This looks fine. When you run that xfmrot command directly on
>>>> the linux command line, do you get the same error?
>>>>
>>>> --
>>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
>>>> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine Damme [
>>>> katherine.da...@gmail.com]
>>>> *Sent:* Wednesday, December 07, 2016 12:41 PM
>>>> *To:* Freesurfer support list
>>>> *Subject:* Re: [Freesurfer] Tracula Set: No Match
>>>>
>>>>
>>>>
>>>> On Mon, Dec 5, 2016 at 12:00 PM, Yendiki, Anastasia <
>>>> ayend...@mgh.harvard.edu> wrote:
>>>>
>>>>> Hi Katherine - The error occurs when processing this file:
>>>

Re: [Freesurfer] Tracula Set: No Match

[Katherine Damme]

On Tue, Dec 13, 2016 at 8:34 AM, Yendiki, Anastasia <
ayend...@mgh.harvard.edu> wrote:

> Ok, if you also send me the first file, /media/Data/Temple/Temple_
> Tracula/31313422_10128/dmri/dwi.ecclog, I'll see if I can replicate the
> error.
>
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine Damme [
> katherine.da...@gmail.com]
> *Sent:* Tuesday, December 13, 2016 9:21 AM
>
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Tracula Set: No Match
>
> Yes. I immediately tried to enter the command in manually, checked the
> paths, and looked at the command manual for any format errors.
>
> [ksd770@katelinux Temple_Tracula]$ xfmrot /media/Data/Temple/Temple_
> Tracula/31313422_10128/dmri/dwi.ecclog /media/Data/Temple/Temple_
> Tracula/31313422_10128/dmri/bvecs.norot /media/Data/Temple/Temple_
> Tracula/31313422_10128/dmri/bvecs
>
> set: No match.
>
> On Wed, Dec 7, 2016 at 2:41 PM, Yendiki, Anastasia <
> ayend...@mgh.harvard.edu> wrote:
>
>> Thanks. This looks fine. When you run that xfmrot command directly on the
>> linux command line, do you get the same error?
>>
>> --
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
>> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine Damme [
>> katherine.da...@gmail.com]
>> *Sent:* Wednesday, December 07, 2016 12:41 PM
>> *To:* Freesurfer support list
>> *Subject:* Re: [Freesurfer] Tracula Set: No Match
>>
>>
>>
>> On Mon, Dec 5, 2016 at 12:00 PM, Yendiki, Anastasia <
>> ayend...@mgh.harvard.edu> wrote:
>>
>>> Hi Katherine - The error occurs when processing this file:
>>> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs.norot
>>>
>>> Can you send this file? Thanks!
>>>
>>> a.y
>>> --
>>> *From:* Katherine Damme [katherine.da...@gmail.com]
>>> *Sent:* Saturday, December 03, 2016 3:42 PM
>>> *To:* Freesurfer support list; Anastasia Yendiki
>>> *Subject:* Tracula Set: No Match
>>>
>>> Hello!
>>>
>>> I have been getting a "set: No match." error. I haven't been able to
>>> sort out what is causing it.
>>>
>>> Attached you will find the configuration file, command, and log files
>>> associated with this error.
>>>
>>> "mv -f /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs
>>> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs.norot
>>> xfmrot /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.ecclog
>>> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs.norot
>>> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs
>>> set: No match."
>>>
>>> ___
>>> 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 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@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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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> add

Re: [Freesurfer] Tracula Set: No Match

[Katherine Damme]

Yes. I immediately tried to enter the command in manually, checked the
paths, and looked at the command manual for any format errors.

[ksd770@katelinux Temple_Tracula]$ xfmrot
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.ecclog
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs.norot
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs

set: No match.

On Wed, Dec 7, 2016 at 2:41 PM, Yendiki, Anastasia <ayend...@mgh.harvard.edu
> wrote:

> Thanks. This looks fine. When you run that xfmrot command directly on the
> linux command line, do you get the same error?
>
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine Damme [
> katherine.da...@gmail.com]
> *Sent:* Wednesday, December 07, 2016 12:41 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Tracula Set: No Match
>
>
>
> On Mon, Dec 5, 2016 at 12:00 PM, Yendiki, Anastasia <
> ayend...@mgh.harvard.edu> wrote:
>
>> Hi Katherine - The error occurs when processing this file:
>> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs.norot
>>
>> Can you send this file? Thanks!
>>
>> a.y
>> --
>> *From:* Katherine Damme [katherine.da...@gmail.com]
>> *Sent:* Saturday, December 03, 2016 3:42 PM
>> *To:* Freesurfer support list; Anastasia Yendiki
>> *Subject:* Tracula Set: No Match
>>
>> Hello!
>>
>> I have been getting a "set: No match." error. I haven't been able to sort
>> out what is causing it.
>>
>> Attached you will find the configuration file, command, and log files
>> associated with this error.
>>
>> "mv -f /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs
>> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs.norot
>> xfmrot /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.ecclog
>> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs.norot
>> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs
>> set: No match."
>>
>> ___
>> 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 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@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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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Tracula Set: No Match

[Katherine Damme]

On Mon, Dec 5, 2016 at 12:00 PM, Yendiki, Anastasia <
ayend...@mgh.harvard.edu> wrote:

> Hi Katherine - The error occurs when processing this file:
> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs.norot
>
> Can you send this file? Thanks!
>
> a.y
> ------
> *From:* Katherine Damme [katherine.da...@gmail.com]
> *Sent:* Saturday, December 03, 2016 3:42 PM
> *To:* Freesurfer support list; Anastasia Yendiki
> *Subject:* Tracula Set: No Match
>
> Hello!
>
> I have been getting a "set: No match." error. I haven't been able to sort
> out what is causing it.
>
> Attached you will find the configuration file, command, and log files
> associated with this error.
>
> "mv -f /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs
> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs.norot
> xfmrot /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.ecclog
> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs.norot
> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs
> set: No match."
>
> ___
> 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 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.
>
>


bvecs.norot
Description: Binary data
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Re: [Freesurfer] Tracula Set: No Match

[Katherine Damme]

Also if I try to avoid this step I get a new error

I don't know if this adds helpful insight!


fslswapdim
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/b0pha.nii.gz x -y z
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/b0pha.nii.gz

INFO: left-right orientation was flipped by fslswapdim

fslorient -forceradiological
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/b0pha.nii.gz

mri_probedicom --i
//media/Data/Temple/Temple_Tracula/31313422_10128/dti_dicom/31313422_10128.MR.Temple.9.1.20140806.182244.xfrp16.dcm
> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/b0info.dat

TE: Subscript out of range.

fslroi
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_eddy.nii.gz
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/lowb.nii.gz 0 1

ERROR: Unrecognized format of phase map
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/b0pha.nii.gz

On Sat, Dec 3, 2016 at 2:42 PM, Katherine Damme <katherine.da...@gmail.com>
wrote:

> Hello!
>
> I have been getting a "set: No match." error. I haven't been able to sort
> out what is causing it.
>
> Attached you will find the configuration file, command, and log files
> associated with this error.
>
> "mv -f /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs
> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs.norot
> xfmrot /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.ecclog
> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs.norot
> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs
> set: No match."
>
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[Freesurfer] qdec long parsing table to look in non-existant directory

[Katherine Damme]

Hello everyone,

I am running qdec for longitudinal data for the first time and although I
have a file that matches the guide on the wiki, the script is looking in a
non-exsistant file location (see below). While there is a 1001 file and a
1001_MR1, I am not sure where it is getting the 1001_MR1.long.1001 dir. Any
ideas?

"long_mris_slopes --qdec long.qdec.table.dat --meas thickness --hemi lh
--do-avg --do-rate --do-pc1 --do-stack --do-label --time years --qcache
fsaverage --sd /home/adapt/Cortical_Thickness_Data

Parsing the qdec table: long.qdec.table.dat

Working in SUBJECTS_DIR: /home/adapt/Cortical_Thickness_Data


Working on hemi: lh


Subject-Template: 1001


INFO: 2 TPs in 1001 , mean age: 0.487704918


===
SUBJECT 1001  Intersecting Within-Subject Cortex Label

ERROR:
/home/adapt/Cortical_Thickness_Data/1001_MR1.long.1001/label/lh.cortex.label
does not exist!"


long.qdec.table.dat
Description: Binary data
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[Freesurfer] Qdec Clusters Graph Extracted

[Katherine Damme]

Hello FreeSurfer Group

I would like to make my own box plot out of a cluster that I identified as
significant in Qdec. Is there any easy way to extract the information that
appears in the graph window so that I can create a box plot?

I've tried extracting it by drawing an roi and using mris_anatomical_stats
and mri_label2label, but the numbers look different than what appears in
the qdec graph.

Any advice would be very appreciated!!

Thank you!

Kate Damme
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Re: [Freesurfer] Tracula: cannot open file `1000' for reading Bedpost file error

[Katherine Damme]

Hello Anastasia, I did specify the files. I used the same config file
(attached) a few months ago to write make a tracula image and then the
dpath was deleted by mistake and when I tried to rerun the same file it is
giving me this error.

On Fri, Mar 6, 2015 at 6:07 PM, Anastasia Yendiki 
ayend...@nmr.mgh.harvard.edu wrote:


 Hi Katherine - Did you specify the gradient table and b-value table in
 your configuration file? I suspect that the issue is that it can't find
 them.

 a.y

 On Tue, 3 Mar 2015, Katherine Damme wrote:

  Hello Freesurfers,
 
  I recently updated my Freesurfer version and now I am getting an error
 in tracula.
 
  awk: cmd. line:1: fatal: cannot open file `1000' for reading (No such
 file or directory)
 
  Any help would be appreciated.
 
 
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 e-mail
 contains patient information, please contact the Partners Compliance
 HelpLine at
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 properly
 dispose of the e-mail.




090.dmrirc
Description: Binary data
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[Freesurfer] Tracula: cannot open file `1000' for reading Bedpost file error

[Katherine Damme]

Hello Freesurfers,

I recently updated my Freesurfer version and now I am getting an error in
tracula.

awk: cmd. line:1: fatal: cannot open file `1000' for reading (No such file
or directory)

Any help would be appreciated.


trac-all.error
Description: Binary data
Mon Mar  2 18:24:56 CST 2015
/home/k/ksd770/Desktop/Subj/090
/usr/local/freesurfer/bin/trac-all
-prep -c 090.dmrirc
Subject 090
SUBJECTS_DIR /home/k/ksd770/Desktop/Subj
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
root
kate.ad.wcas.northwestern.edu
Linux kate.ad.wcas.northwestern.edu 2.6.32-504.8.1.el6.x86_64 #1 SMP Fri Dec 19 12:09:25 EST 2014 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize10240 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc  126968 

 total   used   free sharedbuffers cached
Mem:  16275144   103039725971172  12916  896047644376
-/+ buffers/cache:2569992   13705152
Swap:  8208380  748248133556


Program versions:
$Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $
mri_convert --all-info 
ProgramName: mri_convert  ProgramArguments: --all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2015/03/03-00:24:56-GMT  BuildTimeStamp: May 13 2013 18:45:07  CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $  User: root  Machine: kate.ad.wcas.northwestern.edu  Platform: Linux  PlatformVersion: 2.6.32-504.8.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 30400 
FLIRT version 6.0
$Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
$Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $
ProgramName: dmri_train  ProgramArguments: --all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2015/03/03-00:24:56-GMT  BuildTimeStamp: May 13 2013 18:45:07  CVS:   User: root  Machine: kate.ad.wcas.northwestern.edu  Platform: Linux  PlatformVersion: 2.6.32-504.8.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 30400 
ProgramName: dmri_paths  ProgramArguments: --all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2015/03/03-00:24:56-GMT  BuildTimeStamp: May 13 2013 18:45:07  CVS:   User: root  Machine: kate.ad.wcas.northwestern.edu  Platform: Linux  PlatformVersion: 2.6.32-504.8.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 30400 
ProgramName: dmri_pathstats  ProgramArguments: --all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2015/03/03-00:24:56-GMT  BuildTimeStamp: May 13 2013 18:45:07  CVS:   User: root  Machine: kate.ad.wcas.northwestern.edu  Platform: Linux  PlatformVersion: 2.6.32-504.8.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 30400 
ProgramName: dmri_mergepaths  ProgramArguments: --all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2015/03/03-00:24:56-GMT  BuildTimeStamp: May 13 2013 18:45:07  CVS:   User: root  Machine: kate.ad.wcas.northwestern.edu  Platform: Linux  PlatformVersion: 2.6.32-504.8.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 30400 
INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /usr/local/freesurfer
Previous: /projects/p20394/software/freesurfer-v5.3.0


New invocation of trac-preproc


root
kate.ad.wcas.northwestern.edu
Linux kate.ad.wcas.northwestern.edu 2.6.32-504.8.1.el6.x86_64 #1 SMP Fri Dec 19 12:09:25 EST 2014 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize10240 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc  126968 

 total   used   free sharedbuffers cached
Mem:  16275144   103163885958756  12916  896047644376
-/+ buffers/cache:2582408   13692736
Swap:  8208380  748248133556

#-
/usr/local/freesurfer/bin/trac-preproc 
#-
#@# Image corrections Mon Mar  2 18:24:57 CST 2015
mri_convert /home/k/ksd770/Desktop/Subj/090/orig/90.MR.FMRI_STUDIES_NUSSLOCK.6.1.20140620.100913.pmv751.dcm /home/k/ksd770/Desktop/Subj/090/dmri/dwi_orig.nii.gz
mri_convert /home/k/ksd770/Desktop/Subj/090/orig/90.MR.FMRI_STUDIES_NUSSLOCK.6.1.20140620.100913.pmv751.dcm /home/k/ksd770/Desktop/Subj/090/dmri/dwi_orig.nii.gz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /home/k/ksd770/Desktop/Subj/090/orig/90.MR.FMRI_STUDIES_NUSSLOCK.6.1.20140620.100913.pmv751.dcm...
Getting Series No 
INFO: Found 67 files in /home/k/ksd770/Desktop/Subj/090/orig
INFO: Scanning for Series Number 6
Scanning Directory 
INFO: found 65 files in series
INFO: loading series header info.

RunNo = 5
WARNING: Run 1 appears to be truncated
  Files Found: 65, Files Expected (lRep+1): 1
FileName 		

[Freesurfer] Probabilistic Tractography

[Katherine Damme]

Hello Freesurfer World,

I am trying to decide how to threshold my probabilistic tractography data.

Does anyone have recommendation on best define a threshold?

Thank you,

Kate Damme
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dispose of the e-mail.

Re: [Freesurfer] From bedpostX and recon-all to tracula

[Katherine Damme]

I think so. The attached one is definitely correct.

On Mon, Jan 5, 2015 at 4:01 PM, Anastasia Yendiki 
ayend...@nmr.mgh.harvard.edu wrote:


 Based on the log file, you ran trac-all -prep -c dmrirc.all. The
 configuration that you attached was called dmrirc.all.txt. Are these files
 the same?

 On Mon, 5 Jan 2015, Katherine Damme wrote:

  Sorry I just copied that from remotely accessing my desktop and viewing
 the doc in the terminal. Attached is the complete log.

 On Sat, Jan 3, 2015 at 9:45 PM, Anastasia Yendiki 
 ayend...@nmr.mgh.harvard.edu wrote:

   There should be a few more lines at the top of the log file,
 showing the exact trac-all command line that was executed,
   etc. Is this the entire log file?

   On Sat, 3 Jan 2015, Katherine Damme wrote:

 Here is the log.

 On Sat, Jan 3, 2015 at 9:19 AM, Anastasia Yendiki
 ayend...@nmr.mgh.harvard.edu wrote:

   It looks like it's not finding the file that you
 specify - not
   like it's finding it but it's in the wrong format. But
 I can't
   tell just from one line, I need to see the entire
 output of
   trac-all, which is saved in trac-all.log.

   On Fri, 2 Jan 2015, Katherine Damme wrote:

 I still get the error:
 mv -f
 /home/k/ksd770/Desktop/Subj/
 042/dmri/dwi_orig_flip.mghdti.bvecs
 /home/k/ksd770/Desktop/Subj/042/dmri/bvecs
 mv: cannot stat
 `/home/k/ksd770/Desktop/Subj/
 042/dmri/dwi_orig_flip.mghdti.bvecs':
 No such
 file or directory
 Linux kate.ad.wcas.northwestern.edu
 2.6.32-431.3.1.el6.x86_64 #1 SMP Fri Dec
 13 06:58:20 EST 2013 x86_64 x86_64 x86_64
 GNU/Linux

 trac-preproc exited with ERRORS at Fri Jan  2
 18:55:26 CST 2015

 Is there a way to avoid specifying a bvec/bval
 file
 and allowing it to pull
 this information from the dicom?

 The bvec/bval files that I was specifying came
 from
 previous processing of
 the data with FSL-bedpost, could this be causing
 the
 error?

 On Wed, Dec 31, 2014 at 8:05 PM, Anastasia Yendiki
 ayend...@nmr.mgh.harvard.edu wrote:

   You need to follow the format of
   $FREESURFER_HOME/bin/dmrirc.example. Enter
 single files for
   bvalfile and bvecfile, not lists of files.

   On Wed, 31 Dec 2014, Katherine Damme wrote:

 Now it is crashing giving me an if:
 Expression
 Syntax Error. See below

 On Wed, Dec 31, 2014 at 7:27 PM,
 Anastasia Yendiki
 ayend...@nmr.mgh.harvard.edu wrote:

   Hi Kate - It's not finding the
 gradient table.
 You'll have to
   specify the gradient table and
 b-value table
 as you did for the
   first subject.

   You can use the same config file
 for all your
 subjects, see the
   example in
 $FREESURFER_HOME/bin/dmrirc.example.

   Happy new year,
   a.y

   On Wed, 31 Dec 2014, Katherine
 Damme wrote:

 Hello Everyone!

 I was able to get tracula
 to
 run on one
 subject but
 I am now getting the
 following error with my
 new
 subjects.

 mv: cannot stat


 `/home/k/ksd770/Desktop/Subj/
 043/dmri/dwi_orig_flip.mghdti.bvecs':
 No such
 file or directory

 Let me know

[Freesurfer] FS/Diffusion dwi-infodump.dat error

[Katherine Damme]

Hello Freesurfer Users,

I have been attempting to use the DWI prep steps described under
FS/Diffusion http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Diffusion,
but have gotten the following error.

ERROR: cannot extract sWiPMemBlock.alFree[8] from
/home/k/ksd770/Desktop/Subj/041/dtrecon/dwi-infodump.dat


Thanks for any advice!
dt_recon --i 
$SUBJECTS_DIR/041/orig/041.MR.Reward.8.1.20120529.161930.1yxzlsm.dcm --s 041 
--o $SUBJECTS_DIR/041/dtrecon
INFO: SUBJECTS_DIR is /home/k/ksd770/Desktop/Subj
dt_recon logfile
Mon Jan  5 19:23:07 CST 2015
VERSION $Id: dt_recon,v 1.15 2011/01/25 21:53:04 greve Exp $
setenv SUBJECTS_DIR /home/k/ksd770/Desktop/Subj
cd /home/k/ksd770/Desktop/Subj
/usr/local/freesurfer/bin/dt_recon --i 
/home/k/ksd770/Desktop/Subj/041/orig/041.MR.Reward.8.1.20120529.161930.1yxzlsm.dcm
 --s 041 --o /home/k/ksd770/Desktop/Subj/041/dtrecon
kate.ad.wcas.northwestern.edu
root
/usr/local/fsl/bin/eddy_correct
ECRefTP 0
#@#---
Converting input
Mon Jan  5 19:23:07 CST 2015
cd /home/k/ksd770/Desktop/Subj
mri_convert 
/home/k/ksd770/Desktop/Subj/041/orig/041.MR.Reward.8.1.20120529.161930.1yxzlsm.dcm
 /home/k/ksd770/Desktop/Subj/041/dtrecon/dwi.nii
mri_convert 
/home/k/ksd770/Desktop/Subj/041/orig/041.MR.Reward.8.1.20120529.161930.1yxzlsm.dcm
 /home/k/ksd770/Desktop/Subj/041/dtrecon/dwi.nii 
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from 
/home/k/ksd770/Desktop/Subj/041/orig/041.MR.Reward.8.1.20120529.161930.1yxzlsm.dcm...
crypt_gkey = *CU2sGiIeIxlk
Getting Series No 
INFO: Found 67 files in /home/k/ksd770/Desktop/Subj/041/orig
INFO: Scanning for Series Number 8
Scanning Directory 
INFO: found 65 files in series
INFO: loading series header info.

RunNo = 7
WARNING: Run 1 appears to be truncated
  Files Found: 65, Files Expected (lRep+1): 1
FileName
/home/k/ksd770/Desktop/Subj/041/orig/041.MR.Reward.8.1.20120529.161930.1yxzlsm.dcm
Identification
NumarisVersyngo MR B17
ScannerModel  TrioTim 
PatientName   041 
Date and time
StudyDate 20120529
StudyTime 161930.89 
SeriesTime173154.531000 
AcqTime   172834.645000 
Acquisition parameters
PulseSeq  *ep_b0
Protocol  DTI_64_DIRECTIONS 
PhEncDir  COL
EchoNo1
FlipAngle 90
EchoTime  87
InversionTime -1
RepetitionTime9600
PhEncFOV  224
ReadoutFOV260
Image information
RunNo 7
SeriesNo  8
ImageNo   1
NImageRows1008
NImageCols1170
NFrames   65
SliceArraylSize   72
IsMosaic  1
ImgPos.0483 1086.6573  73.5215 
VolRes  2.   2.   2. 
VolDim130  112   72 
Vc -0.9983  -0.0572   0.0090 
Vr  0.0554  -0.9890  -0.1374 
Vs  0.0168  -0.1367   0.9905 
VolCenter   0.   0.   0. 
TransferSyntaxUID 1.2.840.10008.1.2.1
INFO: sorting.
INFO: (130 112  72), nframes = 65, ismosaic=1
Could not parse NUMARIS version string syngo MR B17
found in dicom tag 18,1020 (len = 3 != 6)
Repetition Time = 9600, TR = 9600 ms
PE Dir COL COL
AutoAlign matrix detected 
AutoAlign Matrix - 
 0.99801  -0.05463  -0.03141   3.84059;
 0.05892   0.98569   0.15796  -22.68560;
 0.02234  -0.15949   0.98695   4.13057;
 0.0   0.0   0.0   1.0;

FileName
/home/k/ksd770/Desktop/Subj/041/orig/041.MR.Reward.8.1.20120529.161930.1yxzlsm.dcm
Identification
NumarisVersyngo MR B17
ScannerModel  TrioTim 
PatientName   041 
Date and time
StudyDate 20120529
StudyTime 161930.89 
SeriesTime173154.531000 
AcqTime   172834.645000 
Acquisition parameters
PulseSeq  *ep_b0
Protocol  DTI_64_DIRECTIONS 
PhEncDir  COL
EchoNo1
FlipAngle 90
EchoTime  87
InversionTime -1
RepetitionTime9600
PhEncFOV  224
ReadoutFOV260
Image information
RunNo 7
SeriesNo  8
ImageNo   1
NImageRows1008
NImageCols1170
NFrames   65
SliceArraylSize   72
IsMosaic  1
ImgPos122.4754 141.0387 -40.2529 
VolRes  2.   2.   2. 
VolDim130  112   72 
Vc -0.9983  -0.0572   0.0090 
Vr  0.0554  -0.9890  -0.1374 
Vs  0.0168  -0.1367   0.9905 

Re: [Freesurfer] From bedpostX and recon-all to tracula

[Katherine Damme]

Hello Everyone!

I was able to get tracula to run on one subject but I am now getting the
following error with my new subjects.

mv: cannot stat
`/home/k/ksd770/Desktop/Subj/043/dmri/dwi_orig_flip.mghdti.bvecs': No such
file or directory

Let me know if you have any ideas why it is not makeing the
dwi_orig_flip.mghdti.bvecs in the prep

Thank you and have a Happy New Year!!!

On Thu, Dec 18, 2014 at 5:38 PM, Anastasia Yendiki 
ayend...@nmr.mgh.harvard.edu wrote:


 Hi Kate - The option to use row-formatted (instead of column-formatted)
 gradient tables was added in a tracula update that came out after
 freesurfer 5.3 was released. If you want to use this format, you can
 download the update here:
 http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates

 You should make sure to download the same build as your 5.3 build, which
 should be the CentOS 6 64-bit, based on this line that I got from your
 trac-all.log:

 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

 a.y


 On Wed, 17 Dec 2014, Katherine Damme wrote:

  Thanks! That was exactly it! It was a FAT server and so that resolved
 that issue.

 Tracula is claiming that the bvecs and bvals don't have the same number
 of entries. These were the bvecs and bval files created during the
 trac-all prep process, but when I preprocesed the data previously with
 FSL the bvecs and bvals that were created did have equal numbers. I
 tried to specify to use these fsl made bvecs and bvals in the
 configuration file and it continues to default to the ones that it made.

  Any ideas?

 Thank you!

 Kate

 On Mon, Dec 15, 2014 at 7:42 PM, Watson, Christopher 
 christopher.wat...@childrens.harvard.edu wrote:
   I think certain filesystems don't support sym linking (e.g. FAT32).
 So that might be it.

   
   From: freesurfer-boun...@nmr.mgh.harvard.edu [
 freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine Damme
   [katherine.da...@gmail.com]
   Sent: Monday, December 15, 2014 5:29 PM
   To: Anastasia Yendiki
   Cc: Freesurfer support list
   Subject: Re: [Freesurfer] From bedpostX and recon-all to tracula

   After removing this I have a new (possibly unrelated error):
   mv -f /media/Sokol/Subj/041/dmri/bvecs /media/Sokol/Subj/041/dmri/
 bvecs.norot
   xfmrot /media/Sokol/Subj/041/dmri/dwi.ecclog
 /media/Sokol/Subj/041/dmri/bvecs.norot /media/Sokol/Subj/041/dmri/bvecs
   ln -sf /media/Sokol/Subj/041/dmri/dwi.nii.gz
 /media/Sokol/Subj/041/dmri/data.nii.gz
   ln: creating symbolic link `/media/Sokol/Subj/041/dmri/data.nii.gz':
 Operation not permitted

   This persists even when I run the command as the root user and
 regardless of the permissions settings of the folder and the
   fdwi.nii.gz file.

   Any ideas?

   On Mon, Dec 15, 2014 at 3:07 PM, Anastasia Yendiki 
 ayend...@nmr.mgh.harvard.edumailto:ayend...@nmr.mgh.harvard.edu wrote:

   It's hard to tell what's causing the error without seeing the
 entire trac-all.log. However, by glancing at your config file
   you seem to still have B0 inhomogeneity correction turned on (dob0
 = 1) but without specifying any field map dicoms. I'd turn
   it off and see if that fixes it.


   On Mon, 15 Dec 2014, Katherine Damme wrote:

   Where would I be specifying a directory as an input/output?

   I used the following cmd: /usr/local/freesurfer/bin/trac-all -prep
 -c dmri.fy

   On Sun, Dec 14, 2014 at 7:12 PM, Bruce Fischl 
 fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote:
 Hi Katerine

 the COR-* format is an old one that we don't use anymore. If
 you specify a directory as an
 input/output we will assume that it contains COR files, which
 is probably what you are seeing.

 cheers
 Bruce


 On Sun, 14 Dec 2014, Katherine Damme wrote:

   At what point is the COR-*.info file made?
   I got the following error:

   corRead(): can't open file /media/Sokol/Subj/COR-.info
   $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16
 mreuter Exp $
   reading from /media/Sokol/Subj/...
   Linux kate.ad.wcas.northwestern.edu
 http://kate.ad.wcas.northwestern.edu 2.6.32-431.3.1.el6.x86_64 #1 SMP
 Fri Dec
   13 06:58:20 EST 2013 x86_64 x86_64 x86_64 GNU/Linux

   trac-preproc exited with ERRORS at Fri Dec 12 12:54:40
 CST 2014

   [ksd770@kate 041]# ls /media/Sokol/Subj/COR-*

   On Thu, Dec 11, 2014 at 2:48 PM, Anastasia Yendiki
   ayend...@nmr.mgh.harvard.edumailto:ayend...@nmr.mgh.
 harvard.edu wrote:

 No, those are field maps used to correct for
 inhomogeneities in
 the main magnetic field (which in MRI lingo is
 referred

Re: [Freesurfer] From bedpostX and recon-all to tracula

[Katherine Damme]

Where would I be specifying a directory as an input/output?

I used the following cmd: /usr/local/freesurfer/bin/trac-all -prep -c
dmri.fy

On Sun, Dec 14, 2014 at 7:12 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:

 Hi Katerine

 the COR-* format is an old one that we don't use anymore. If you specify a
 directory as an input/output we will assume that it contains COR files,
 which is probably what you are seeing.

 cheers
 Bruce



 On Sun, 14 Dec 2014, Katherine Damme wrote:

  At what point is the COR-*.info file made?
 I got the following error:

 corRead(): can't open file /media/Sokol/Subj/COR-.info
 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
 reading from /media/Sokol/Subj/...
 Linux kate.ad.wcas.northwestern.edu 2.6.32-431.3.1.el6.x86_64 #1 SMP Fri
 Dec
 13 06:58:20 EST 2013 x86_64 x86_64 x86_64 GNU/Linux

 trac-preproc exited with ERRORS at Fri Dec 12 12:54:40 CST 2014

 [ksd770@kate 041]# ls /media/Sokol/Subj/COR-*

 On Thu, Dec 11, 2014 at 2:48 PM, Anastasia Yendiki
 ayend...@nmr.mgh.harvard.edu wrote:

   No, those are field maps used to correct for inhomogeneities in
   the main magnetic field (which in MRI lingo is referred to as
   the B0 field, not to be confused with the b=0 images). You can
   skip that correction (you have to skip it if you don't have
   field maps).

   On Thu, 11 Dec 2014, Katherine Damme wrote:

 I am sorry, I am a bit confused. What am I supposed
 to be specifying under
 the b0mlist and b0plist?

 I thought that it was the B0 low-b image from
 diffusion.

 Thank you!

 On Thu, Dec 11, 2014 at 2:25 PM, Anastasia Yendiki
 ayend...@nmr.mgh.harvard.edu wrote:

   Hi Kate - The screenshot looks more like a
 low-b image from a
   diffusion scan than a field map. In case this
 helps, the phase
   map data will have either 2 volumes (2 phase
 maps acquired at
   different echo times) or 1 volume (the
 difference of 2 such
   phase maps).

   Best,
   a.y

   On Thu, 11 Dec 2014, Katherine Damme wrote:

 Hello


 Has anyone else had the problem of
 tracula not
 recognizing the format of the
 phase map?

  I opened the B0 in fslview and it
 appeared normal
 (see screenshot). Any
 help that you can offer would be greatly
 appreciated! Thank you!

 Thank you!

 Kate Damme


 On Fri, Nov 21, 2014 at 4:02 PM,
 Anastasia Yendiki
 ayend...@nmr.mgh.harvard.edu wrote:

   Hi Kate - The -prep, -bedp, and
 -path steps
 need to be run
   separately, in that order. You
 can't run them
 all at once
   unfortunately. See:



 http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/
 RunningTracula

   a.y

   On Wed, 29 Oct 2014, Katherine
 Damme wrote:

 Sorry for the delay. I
 signed up for the
 course and
 hoped that it would answer
 my question,
 but I am
 still
 unsure what went wrong.

 Thank you.

 On Tue, Sep 9, 2014 at 12:14
 PM,
 Anastasia Yendiki

 ayend...@nmr.mgh.harvard.edu wrote:

   Can you please attach
 the
 trac-all.log file,
 which has the entire output
 from
 beginning to end?
   Ofter something goes
 wrong earlier
 that causes
 the program to fail later in
 the
 process.

   Also, we'll need your
 original
 configuration
 file. Thanks!

   On Mon, 8 Sep 2014,
 Katherine
 Damme wrote:

 Hello Freesurfer
 Community

Re: [Freesurfer] From bedpostX and recon-all to tracula

[Katherine Damme]

At what point is the COR-*.info file made?

I got the following error:

corRead(): can't open file /media/Sokol/Subj/COR-.info
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /media/Sokol/Subj/...
Linux kate.ad.wcas.northwestern.edu 2.6.32-431.3.1.el6.x86_64 #1 SMP Fri
Dec 13 06:58:20 EST 2013 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Fri Dec 12 12:54:40 CST 2014

[ksd770@kate 041]# ls /media/Sokol/Subj/COR-*

On Thu, Dec 11, 2014 at 2:48 PM, Anastasia Yendiki 
ayend...@nmr.mgh.harvard.edu wrote:


 No, those are field maps used to correct for inhomogeneities in the main
 magnetic field (which in MRI lingo is referred to as the B0 field, not to
 be confused with the b=0 images). You can skip that correction (you have to
 skip it if you don't have field maps).


 On Thu, 11 Dec 2014, Katherine Damme wrote:

  I am sorry, I am a bit confused. What am I supposed to be specifying under
 the b0mlist and b0plist?

 I thought that it was the B0 low-b image from diffusion.

 Thank you!

 On Thu, Dec 11, 2014 at 2:25 PM, Anastasia Yendiki
 ayend...@nmr.mgh.harvard.edu wrote:

   Hi Kate - The screenshot looks more like a low-b image from a
   diffusion scan than a field map. In case this helps, the phase
   map data will have either 2 volumes (2 phase maps acquired at
   different echo times) or 1 volume (the difference of 2 such
   phase maps).

   Best,
   a.y

   On Thu, 11 Dec 2014, Katherine Damme wrote:

 Hello


 Has anyone else had the problem of tracula not
 recognizing the format of the
 phase map?

  I opened the B0 in fslview and it appeared normal
 (see screenshot). Any
 help that you can offer would be greatly
 appreciated! Thank you!

 Thank you!

 Kate Damme


 On Fri, Nov 21, 2014 at 4:02 PM, Anastasia Yendiki
 ayend...@nmr.mgh.harvard.edu wrote:

   Hi Kate - The -prep, -bedp, and -path steps
 need to be run
   separately, in that order. You can't run them
 all at once
   unfortunately. See:


 http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/
 RunningTracula

   a.y

   On Wed, 29 Oct 2014, Katherine Damme wrote:

 Sorry for the delay. I signed up for the
 course and
 hoped that it would answer my question,
 but I am
 still
 unsure what went wrong.

 Thank you.

 On Tue, Sep 9, 2014 at 12:14 PM,
 Anastasia Yendiki
 ayend...@nmr.mgh.harvard.edu wrote:

   Can you please attach the
 trac-all.log file,
 which has the entire output from
 beginning to end?
   Ofter something goes wrong earlier
 that causes
 the program to fail later in the
 process.

   Also, we'll need your original
 configuration
 file. Thanks!

   On Mon, 8 Sep 2014, Katherine
 Damme wrote:

 Hello Freesurfer Community!

 Thank you Anastasia and
 Christopher, I
 am still getting ending with errors and
 the log
 file gives no clue that I
 have been able
 to detect, see attached.

 Any help would be
 appreciated!


 On Thu, Sep 4, 2014 at 4:29
 PM,
 Anastasia Yendiki
 ayend...@nmr.mgh.harvard.edu
 wrote:

   Hi Kate - There is an
 example
 configuration file for tracula in your
   freesurfer
 distribution
 ($FREESURFER_HOME/bin/dmrirc.example).
 The same
   file is also here:


 http://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc

   If you attach your
 configuration
 file and the log file

 (scripts/trac-all.log), we can try
 to troubleshoot.

   a.y

   On Wed, 3 Sep 2014,
 Katherine
 Damme wrote:

Hello

Re: [Freesurfer] From bedpostX and recon-all to tracula

[Katherine Damme]

I am sorry, I am a bit confused. What am I supposed to be specifying under
the b0mlist and b0plist?

I thought that it was the B0 low-b image from diffusion.

Thank you!

On Thu, Dec 11, 2014 at 2:25 PM, Anastasia Yendiki 
ayend...@nmr.mgh.harvard.edu wrote:


 Hi Kate - The screenshot looks more like a low-b image from a diffusion
 scan than a field map. In case this helps, the phase map data will have
 either 2 volumes (2 phase maps acquired at different echo times) or 1
 volume (the difference of 2 such phase maps).

 Best,
 a.y


 On Thu, 11 Dec 2014, Katherine Damme wrote:

  Hello


 Has anyone else had the problem of tracula not recognizing the format of
 the
 phase map?

  I opened the B0 in fslview and it appeared normal (see screenshot). Any
 help that you can offer would be greatly appreciated! Thank you!

 Thank you!

 Kate Damme


 On Fri, Nov 21, 2014 at 4:02 PM, Anastasia Yendiki
 ayend...@nmr.mgh.harvard.edu wrote:

   Hi Kate - The -prep, -bedp, and -path steps need to be run
   separately, in that order. You can't run them all at once
   unfortunately. See:

   http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RunningTracula

   a.y

   On Wed, 29 Oct 2014, Katherine Damme wrote:

 Sorry for the delay. I signed up for the course and
 hoped that it would answer my question, but I am
 still
 unsure what went wrong.

 Thank you.

 On Tue, Sep 9, 2014 at 12:14 PM, Anastasia Yendiki
 ayend...@nmr.mgh.harvard.edu wrote:

   Can you please attach the trac-all.log file,
 which has the entire output from beginning to end?
   Ofter something goes wrong earlier that causes
 the program to fail later in the process.

   Also, we'll need your original configuration
 file. Thanks!

   On Mon, 8 Sep 2014, Katherine Damme wrote:

 Hello Freesurfer Community!

 Thank you Anastasia and Christopher, I
 am still getting ending with errors and the log
 file gives no clue that I have been able
 to detect, see attached.

 Any help would be appreciated!


 On Thu, Sep 4, 2014 at 4:29 PM,
 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
 wrote:

   Hi Kate - There is an example
 configuration file for tracula in your
   freesurfer distribution
 ($FREESURFER_HOME/bin/dmrirc.example). The same
   file is also here:

 http://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc

   If you attach your configuration
 file and the log file
   (scripts/trac-all.log), we can try
 to troubleshoot.

   a.y

   On Wed, 3 Sep 2014, Katherine
 Damme wrote:

Hello Freesurfer Community!
I have sucessfully completed
 diffusion preprocessing in FSL and the
recon-all of the structural
 image and would like to use tracula for the
tract reconstruction. I keep
 having trouble with my configuration file.
   
Does anyone have a bedpostX
 tracula config file they could share as an
example?H
   
Thank you!
   
Kate
   
   

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Re: [Freesurfer] From bedpostX and recon-all to tracula

[Katherine Damme]

Hello Freesurfer Community!

Thank you Anastasia and Christopher, I am still getting ending with errors
and the log file gives no clue that I have been able to detect, see
attached.

Any help would be appreciated!


On Thu, Sep 4, 2014 at 4:29 PM, Anastasia Yendiki 
ayend...@nmr.mgh.harvard.edu wrote:


 Hi Kate - There is an example configuration file for tracula in your
 freesurfer distribution ($FREESURFER_HOME/bin/dmrirc.example). The same
 file is also here:
 http://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc

 If you attach your configuration file and the log file
 (scripts/trac-all.log), we can try to troubleshoot.

 a.y

 On Wed, 3 Sep 2014, Katherine Damme wrote:

  Hello Freesurfer Community!
  I have sucessfully completed diffusion preprocessing in FSL and the
  recon-all of the structural image and would like to use tracula for the
  tract reconstruction. I keep having trouble with my configuration file.
 
  Does anyone have a bedpostX tracula config file they could share as an
  example?H
 
  Thank you!
 
  Kate
 
 
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 The information in this e-mail is intended only for the person to whom it
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 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.




trac-all.error
Description: Binary data


dmrirc.local
Description: Binary data
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] From bedpostX and recon-all to tracula

[Katherine Damme]

Hello Freesurfer Community!

I have sucessfully completed diffusion preprocessing in FSL and the
recon-all of the structural image and would like to use tracula for the
tract reconstruction. I keep having trouble with my configuration file.

Does anyone have a bedpostX tracula config file they could share as an
example?

Thank you!

Kate
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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.