[Freesurfer] White matter hypointensities

[Rockers, Elijah D.]

External Email - Use Caution

Hello,

When was the wm-hypointeisities label added to the Freesurfer segmentation? Is 
there any paper that explicitly mentions this, or should I just cite the 2002 
paper?

Thanks,
-Eli

Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & 
World Report as the No. 1 hospital in Texas and among the top 20 hospitals 
nationwide. Houston Methodist is the only nationally ranked Honor Roll hospital 
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[Freesurfer] qdec / tksurfer GUI

[Rockers, Elijah D.]

External Email - Use Caution

I've noticed an issue when trying to manually input values into fields with 
Qdec. This problem has been reported before. I thought perhaps it was because 
Qdec is deprecated, so I loaded the results into tksurfer, and I can't change 
fields in this program either. It's as if the keyboard is not recognized. Mouse 
input has no problem.

For isntance, if I try to use the "Save Multiple Views as TIFFs ... " tool, I 
can't even type in a filename. Nor can I change threshold levels on the overlay 
configuration (besides dragging the threshold markers, which is less accurate 
than I need).

Any suggestions on how I might debug this?

Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & 
World Report as the No. 1 hospital in Texas and among the top 20 hospitals 
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[Freesurfer] freeview command line options

[Rockers, Elijah D.]

External Email - Use Caution

Hello, it's possible I found a bug in freeview:

I'm using the overlay_color option with freeview. Specifically I am trying to 
use both the "truncate" and "inverse" options in a command line call to 
freeview for a pipeline I am building. The documentation says that I can apply 
more than one, delimited by commas  however I have found that if I attempt 
to use both truncate and inverse, it seems to be only applying whichever one 
appears last on the list.

In an interactive instance of freeview, doing everything manually, I have no 
problems. Just seems to be an issue with the command line call. Any suggestions 
on how I might proceed in this case?

-Eli

Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & 
World Report as the No. 1 hospital in Texas and among the top 20 hospitals 
nationwide. Houston Methodist is the only nationally ranked Honor Roll hospital 
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[Freesurfer] mri_glmfit: don't display "positive"

[Rockers, Elijah D.]

External Email - Use Caution

Hello,

with Qdec, there was an  option to "remove" positive (or negative) results from 
the displayed overlay...

Is it possible to do something similar with the results of mri_glmfit, but 
displaying with freeview instead? For instance, if I wanted to exclude regions 
that appear to have increased cortical thickness when compared to healthy 
controls?

Thanks,
Eli

Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & 
World Report as the No. 1 hospital in Texas and among the top 20 hospitals 
nationwide. Houston Methodist is the only nationally ranked Honor Roll hospital 
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[Freesurfer] T1 hypointensities

[Rockers, Elijah D.]

External Email - Use Caution

Hello,


Are the WM-hypointensities segmented in the same way as the rest of the 
subcortical regions? i.e., using the probablistic atlas referenced in the 2002 
Fischl et al paper?


Thanks,

- Eli

Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & 
World Report as the No. 1 hospital in Texas for patient care. Houston Methodist 
is nationally ranked in 8 specialties and is designated as a Magnet hospital 
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[Freesurfer] surface arithmetic?

[Rockers, Elijah D.]

External Email - Use Caution

Hello,


I have a subject with two MRIs and surface reconstructions, several years 
apart. I would like to directly compare these surfaces if possible, for 
instance, to subtract (new - old) to see a "difference surface" or something 
similar. Is there a way to A) Get the surfaces into the same space so they can 
be combined mathematically, and B) performs operations with the surfaces, a la 
fslmaths?


Many thanks,

- Eli

Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & 
World Report as the No. 1 hospital in Texas for patient care. Houston Methodist 
is nationally ranked in 8 specialties and is designated as a Magnet hospital 
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Re: [Freesurfer] Surface editing: recon-all exited with errors

[Rockers, Elijah D.]

External Email - Use Caution

Hi Andrew,


Looks like that cleared the errors.


Thank you both,

-Eli


From: Hoopes, Andrew 
Sent: Tuesday, July 31, 2018 3:09 PM
To: Freesurfer support list
Cc: Rockers, Elijah D.
Subject: Re: [Freesurfer] Surface editing: recon-all exited with errors

Hi Eli, the -make all flag contains a bug in the 6.0 release. This can be fixed 
if you download this script - 
https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.edu_pub_dist_freesurfer_dev-5Fbinaries_centos6-5Fx86-5F64_recon-2Dall.makefile=DwIGaQ=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q=NdmdZKAguIV8eXD4q6jw5Ub-tV1C8ZYAQonZaC5Moj4=OVTOQexQaYiTh7MsmChOewxSfa3PnCfztVjr2RDlnM8=
 - and overwrite the current $FREESURFER_HOME/bin/recon-all.makefile

Let me know if you still have issues

best,
Andrew


On 7/31/18, 3:15 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Bruce Fischl"  wrote:

h, maybe -make all has changed (or my memory of what it does is
incorrect). I'll find someone else here to help you out

cheers
Bruce
On Tue, 31 Jul 2018,
Bruce Fischl wrote:

> did you run
>
> recon-all -s  -make all
>
> ?
>
>
> I don't see it in the log
    > On Tue, 31 Jul 2018, Rockers, Elijah D. wrote:
>
>>
>>  External Email - Use Caution
>>
>>  Oh, yep, sorry about that. I copy the list on this e-mail, and attach 
the
>>  log. I think the list
>>  blocks attachments, but if anyone wants to see full log I can send it.
>>
>>
>>  Thanks to all,
>>
>>  -Eli
>>


Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & 
World Report as the No. 1 hospital in Texas for patient care. Houston Methodist 
is nationally ranked in 8 specialties and is designated as a Magnet hospital 
for excellence in nursing.  Visit us at  houstonmethodist.org. Follow us at  
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Re: [Freesurfer] Surface editing: recon-all exited with errors

[Rockers, Elijah D.]

External Email - Use Caution

Yeah, we have an XNAT instance which can automatically run "recon-all -all" on 
new incoming images.


Then I download the subject Freesurfer folder from that database, and edit the 
surfaces (following the tutorial on the freesurfer site), then I run recon-all 
-make all on to "update" the reconstruction for that subject. I have done this 
successfully many times in the past with no issues. Not sure what is different 
now.


Thanks,

- Eli


From: Bruce Fischl 
Sent: Tuesday, July 31, 2018 2:14:18 PM
To: Freesurfer support list
Cc: Rockers, Elijah D.
Subject: Re: [Freesurfer] Surface editing: recon-all exited with errors

h, maybe -make all has changed (or my memory of what it does is
incorrect). I'll find someone else here to help you out

cheers
Bruce
On Tue, 31 Jul 2018,
Bruce Fischl wrote:

> did you run
>
> recon-all -s  -make all
>
> ?
>
>
> I don't see it in the log
> On Tue, 31 Jul 2018, Rockers, Elijah D. wrote:
>
>>
>>  External Email - Use Caution
>>
>>  Oh, yep, sorry about that. I copy the list on this e-mail, and attach the
>>  log. I think the list
>>  blocks attachments, but if anyone wants to see full log I can send it.
>>
>>
>>  Thanks to all,
>>
>>  -Eli
>>
>>  
>> ____________
>>  From: Bruce Fischl 
>>  Sent: Tuesday, July 31, 2018 2:03:05 PM
>>  To: Rockers, Elijah D.
>>  Subject: Re: Surface editing: recon-all exited with errors
>>  can you cc the list on these emails so others can help?
>>  On Tue, 31 Jul 2018,
>>  Rockers, Elijah D. wrote:
>>
>> >
>> >  External Email - Use Caution
>> >
>> >  The recon-all -make all command finished relatively quickly, still with
>> >  errors. It's still showing
>> >  the same errors, and I have attached the new recon-all.log.
>> >
>> > ___
>>  _
>> >  From: Rockers, Elijah D.
>> >  Sent: Tuesday, July 31, 2018 12:32:11 PM
>> >  To: Bruce Fischl
>> >  Subject: Re: Surface editing: recon-all exited with errors
>> >
>> >  Odd. I assumed the individual recon-all commands in the log are just
>> >  what is reported by the
>>  general
>> >  pipeline, since I definitely did not issue all those commands
>> >  separately. I just used the
>>  recon-all
>> >  -make all command after editing. In anycase, I will run it again to see
>> >  if anything changes, but I
>> >  think that would be surprising.
>> >
>> >
>> >  Thanks again
>> >
>> >  - Eli
>> >
>> > ___
>>  _
>> >  From: Bruce Fischl 
>> >  Sent: Tuesday, July 31, 2018 11:52:59 AM
>> >  To: Rockers, Elijah D.
>> >  Subject: Re: Surface editing: recon-all exited with errors
>> >  Hi Eli
>> >
>> >  it's hard for me to tell since you have so many individual recon-all
>> >  commands, but it looks like you didn't recreate all the surfaces after
>> >  editing. Errors like thiss one:
>> >
>> >  mrisReadTriangleFile(../surf/lh.sphere.reg): surface doesn't match
>> >  ../surf/lh.white.preaparc
>> >
>> >  typically mean something hasn't been recreated properly. Try running
>> >  recon-all -make all
>> >
>> >  cheers
>> >  Bruce
>> >
>> >
>> >  On Tue,
>> >  31 Jul 2018, Rockers, Elijah D. wrote:
>> >
>> > >
>> > >  External Email - Use Caution
>> > >
>> > >  Hi Bruce,
>> > >
>> > >
>> > >  I have attached the recon-all.log, regarding an exit with ERRORS that
>> > >  occured after manually
>> >  editing
>> > >  the surface. Thanks for taking a look.
>> > >
>> > >
>> > >  Also, I double checked - the original recon-all command finished with
>> > >  no errors. So it seems the
>> > >  message occurs after surface editing. But the new reconstructed
>> > >  surfaces appear accurate, at
>>  least
>> > >  with respect to gray and white matter boundaries. Let me know if
>> > >  there's anything else you need.
>> > >
>> > >

[Freesurfer] Surface editing: recon-all exited with errors

[Rockers, Elijah D.]

External Email - Use Caution

Hello.


I manually edited the brainmask.mgz file for three subjects. This was done to 
prevent the pial surface from extending into non-cortical areas, in particular 
the soft-tissue near the brain stem, and some cerebellar areas. Usually this 
type of editing (just removing voxels from brianmask.mgz) doesn't give me any 
trouble, and I use the command recon-all -make all -subjid  -sd 
 to then rebuild the surfaces.


However, the tail of the log shows that the pipeline exited with errors, with a 
few commands near the end related to curvstats and jacobian_white failing. The 
new surfaces seem to look fine in freeview. The edits to brainmask were 
registered correctly, but I'm still concerned that the errors might affect an 
mri_glmfit analysis. This is true for all three subjects I edited, which seems 
odd, and I'm not sure what would be causing this.


Below is a pastebin showing the relevant errors. The rest of the pipeline seems 
to execute without errors. I could send entire log if necessary.


https://pastebin.com/raw/b4JX04AT


Thanks,

- Eli

Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & 
World Report as the No. 1 hospital in Texas for patient care. Houston Methodist 
is nationally ranked in 8 specialties and is designated as a Magnet hospital 
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[Freesurfer] T1 / T2 WMH Segmentation

[Rockers, Elijah D.]

Hello,


I noticed that recon-all automatically segments hypointesities in the white 
matter regions. Is there any possibility of using Freesurfer to segment T2 
FLAIR WMH?


I did not see anything in the Wiki documentation about it.


Thanks,

- Eli

Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & 
World Report as the No. 1 hospital in Texas for patient care. Houston Methodist 
is nationally ranked in 8 specialties and is designated as a Magnet hospital 
for excellence in nursing.  Visit us at  houstonmethodist.org. Follow us at  
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[Freesurfer] mri_convert trying to find DWI parameters from Philips scans

[Rockers, Elijah D.]

Hello,

I am using mri_convert to convert my standard T1-weighted structural images 
into nifti format.

The conversion works, but it might be somewhat delayed due to spamming the 
console with the following message

ERROR: don't know how to get DWI parameters from --Philips Healthcare--
ERROR: GetDICOMInfo(): dcmGetDWIParams() 1
DICOM File: 
sd_withholder/withholder_MRI/scans/1201_T1W_TFE/DICOM/1.3.46.670589.11.42034.5.0.10936.2017012009011821006-1201-95-sktipi.dcm
break DICOMRead.c:5228

As far as I can tell, it spams this message once for each dicom file in the 
directory, and there being hundreds or even thousands of dicom files for a 
single subject, this can get old pretty quick. I think this might be new 
behavior in freesurfer 6, because I don't recall seeing this with 5.3 (although 
I could be wrong)

Is there anyway to disable this?

Thanks,
- Eli

Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & 
World Report as the No. 1 hospital in Texas for patient care. Houston Methodist 
is nationally ranked in 8 specialties and is designated as a Magnet hospital 
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Re: [Freesurfer] reconstruction for very significant atrophy

[Rockers, Elijah D.]

The entire result overlay appears shifted, yes.

Put differently, we are seeing significant results in the regions just a bit 
superior to the regions we know to have atrophy. I am just wondering if there 
is something else I can check in the pipeline to make sure everything is lining 
up correctly before the glmfit analysis. Like just in case some of the subjects 
are not accurately registered into the common space used for the vertex-wise 
analysis.

FYI we are comparing 8 diseased (nonfluent PPA) subjects to ~40 controls. I 
have manually checked the segmentations for all these images, and they are 
accurate.

Thanks for your help,
-Eli

On Thu, 2018-01-11 at 11:43 -0500, freesurfer-requ...@nmr.mgh.harvard.edu wrote:

Message: 3
Date: Thu, 11 Jan 2018 11:02:41 -0500 (EST)
From: Bruce Fischl 
<fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] reconstruction for very significant atrophy
To: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Message-ID:

<alpine.lrh.2.20.180102310.32...@gate.nmr.mgh.harvard.edu<mailto:alpine.lrh.2.20.180102310.32...@gate.nmr.mgh.harvard.edu>>
Content-Type: text/plain; charset="utf-8"

do you mean that the entire surface is off by a fixed amount?
On Thu, 11 Jan
2018, Rockers, Elijah D. wrote:



Thanks Bruce.

I went over some more images with our PI and he was mostly satisfied with the 
pial/white
segmentations. The real problem here is that our results look correct, except 
for they seem to be
translated vertically by a small amount, comparing with what we see on the 
MRIs. What can we check
to make sure everything is lining up correctly?

- Eli

On Thu, 2018-01-11 at 08:08 -0500, 
freesurfer-requ...@nmr.mgh.harvard.edu<mailto:freesurfer-requ...@nmr.mgh.harvard.edu>
 wrote:

Message: 5
Date: Wed, 10 Jan 2018 20:26:11 +
From: "Rockers, Elijah D." 
<edrock...@houstonmethodist.org<mailto:edrock...@houstonmethodist.org>>
Subject: [Freesurfer] reconstruction for very significant atrophy
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Message-ID: 
<1515615971.3868.3.ca...@houstonmethodist.org<mailto:1515615971.3868.3.ca...@houstonmethodist.org>>
Content-Type: text/plain; charset="utf-8"

Hello,

We have some images that reflect severe atrophy in some subjects, in which gray 
matter is virtually
undetectable on the MRI in some regions. However, upon checking the 
segmentations visually, the whit
e/pial surfaces are reflecting a significant cortical thickness in these areas.

Is there perhaps any recon-all setting that might extend the white matter area 
out a little more agg
ressively than it does with the default settings?

Thanks,

- Eli

Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & 
World Report as the No. 1 hospital in Texas for patient care. Houston Methodist 
is nationally ranked in 8 specialties and is designated as a Magnet hospital 
for excellence in nursing.  Visit us at  houstonmethodist.org. Follow us at  
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Re: [Freesurfer] reconstruction for very significant atrophy

[Rockers, Elijah D.]

Thanks Bruce.

I went over some more images with our PI and he was mostly satisfied with the 
pial/white segmentations. The real problem here is that our results look 
correct, except for they seem to be translated vertically by a small amount, 
comparing with what we see on the MRIs. What can we check to make sure 
everything is lining up correctly?

- Eli

On Thu, 2018-01-11 at 08:08 -0500, freesurfer-requ...@nmr.mgh.harvard.edu wrote:

Message: 5
Date: Wed, 10 Jan 2018 20:26:11 +
From: "Rockers, Elijah D." 
<edrock...@houstonmethodist.org<mailto:edrock...@houstonmethodist.org>>
Subject: [Freesurfer] reconstruction for very significant atrophy
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Message-ID: 
<1515615971.3868.3.ca...@houstonmethodist.org<mailto:1515615971.3868.3.ca...@houstonmethodist.org>>
Content-Type: text/plain; charset="utf-8"

Hello,

We have some images that reflect severe atrophy in some subjects, in which gray 
matter is virtually undetectable on the MRI in some regions. However, upon 
checking the segmentations visually, the white/pial surfaces are reflecting a 
significant cortical thickness in these areas.

Is there perhaps any recon-all setting that might extend the white matter area 
out a little more aggressively than it does with the default settings?

Thanks,

- Eli

Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & 
World Report as the No. 1 hospital in Texas for patient care. Houston Methodist 
is nationally ranked in 8 specialties and is designated as a Magnet hospital 
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 and 
https://urldefense.proofpoint.com/v2/url?u=http-3A__facebook.com_HoustonMethodist=DwICAg=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q=CAYGC0ZOLxrUbIrT78SfflAkZfYgzH8oPSEwBFUSUJg=04vdwvZSyWy5SG-GmsAzYUrtI0lyfQC__axac_6TQzM=.
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Message: 6
Date: Wed, 10 Jan 2018 15:28:25 -0500 (EST)
From: Bruce Fischl 
<fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] reconstruction for very significant atrophy
To: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Message-ID:

<alpine.lrh.2.20.1801101527330.32...@gate.nmr.mgh.harvard.edu<mailto:alpine.lrh.2.20.1801101527330.32...@gate.nmr.mgh.harvard.edu>>
Content-Type: text/plain; charset=US-ASCII; format=flowed

Hi Eli

it's hard to say without looking at an image. Can you upload a subject and
point us at a spot you think is incorrect? And do you really think the
thickness should be 0 - there is no gray matter left at all? That seems
unlikely

cheers
Bruce
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[Freesurfer] reconstruction for very significant atrophy

[Rockers, Elijah D.]

Hello,

We have some images that reflect severe atrophy in some subjects, in which gray 
matter is virtually undetectable on the MRI in some regions. However, upon 
checking the segmentations visually, the white/pial surfaces are reflecting a 
significant cortical thickness in these areas.

Is there perhaps any recon-all setting that might extend the white matter area 
out a little more aggressively than it does with the default settings?

Thanks,

- Eli

Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & 
World Report as the No. 1 hospital in Texas for patient care. Houston Methodist 
is nationally ranked in 8 specialties and is designated as a Magnet hospital 
for excellence in nursing.  Visit us at  houstonmethodist.org. Follow us at  
twitter.com/MethodistHosp and facebook.com/HoustonMethodist.  
***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist 
and/or its relevant affiliates and may contain restricted and privileged 
material for the sole use of the intended recipient(s). Any review, use, 
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[Freesurfer] Cortical thickness clarification

[Rockers, Elijah D.]

Hello,

I was hoping to get some clarification on how exactly the cortical thickness 
number is calculated. In the videos, Doug says it's "the distance between the 
vertex on the white to the vertex on the pial, and you go backwards and 
forwards to compute the average thickness", and the 2000 paper says "the 
thickness is computed as the average of this distance measured from each 
surface to the other".

From what I understand, You find the closest vertex on the pial surface from a 
given white matter surface vertex, then calculate the distance both ways and 
take the average. Why is the value not the same both ways, i.e., from white to 
pial, and from pial to white?

Thanks very much,
Eli

Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & 
World Report as the No. 1 hospital in Texas for patient care. Houston Methodist 
is nationally ranked in 8 specialties and is designated as a Magnet hospital 
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Re: [Freesurfer] Hard failure via XNAT pipeline (Freesurfer 6)

[Rockers, Elijah D.]

We'll try to process it on a blade server tongiht... if it succeeds we can edit 
any incorrect results as needed.

The image is from a separate site, it has OK resolution (1x1x1.5) but has an 
enormous amount of gibbs ringing compared to our on-site images, which is 
probably causing the issue...

Thanks,
Eli



Date: Wed, 23 Aug 2017 11:54:06 -0400
From: Bruce Fischl 
<fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Hard failure via XNAT pipeline (Freesurfer
6)
To: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Message-ID: 
<54b7b7a7-cdc3-46f1-8e1b-098142fd3...@nmr.mgh.harvard.edu<mailto:54b7b7a7-cdc3-46f1-8e1b-098142fd3...@nmr.mgh.harvard.edu>>
Content-Type: text/plain; charset="us-ascii"

That defect is so big you probably ran out of memory.

> On Aug 23, 2017, at 11:21 AM, Rockers, Elijah D. 
> <edrock...@houstonmethodist.org<mailto:edrock...@houstonmethodist.org>> wrote:
>
> We encountered a hard failure, below is the tail of the log. We are currently 
> running Freesurfer 6 again locally to see if it succeeds on a desktop machine 
> (this is the first time encountering a hard failure on the XNAT server). Any 
> suggestions?
>
>   -merging segment 180 into 178
> 160 defects to be corrected
> 0 vertices coincident
> reading input surface 
> /data/build/nnac/20170818_114535/alamode_MRI08162017/20170818114538/alamode_MRI08162017/surf/lh.qsphere.nofix...
> reading brain volume from brain...
> reading wm segmentation from wm...
> Computing Initial Surface Statistics
>   -face   loglikelihood: -8.7982  (-4.3991)
>   -vertex loglikelihood: -6.2982  (-3.1491)
>   -normal dot loglikelihood: -3.5611  (-3.5611)
>   -quad curv  loglikelihood: -6.1931  (-3.0965)
>   Total Loglikelihood : -24.8505
>
> CORRECTING DEFECT 0 (vertices=40706, convex hull=11265, v0=89)
> XL defect detected...
> Segmentation fault (core dumped)
> Linux hhvrixnatp01 2.6.32-431.el6.x86_64 #1 SMP Sun Nov 10 22:19:54 EST 2013 
> x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s alamode_MRI08162017 exited with ERRORS at Mon Aug 21 19:27:09 
> CDT 2017
>
> To report a problem, see 
> https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.edu_fswiki_BugReporting=DwIBAg=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q=ZUxVIMrFX5hWNR4618Ng1NGK5pswnaS1K8_SrFxDwio=UPo-wFt-ACmW_p7FRxtgmbsmsxyiC8zWu4xz_jMpwRM=
>
> Houston Methodist. Leading Medicine.
>
> Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital 
> in Texas for patient care. Houston Methodist is nationally ranked in 8 
> specialties and is designated as a Magnet hospital for excellence in nursing. 
> Visit us at houstonmethodist.org. Follow us at 
> https://urldefense.proofpoint.com/v2/url?u=http-3A__twitter.com_MethodistHosp=DwIBAg=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q=ZUxVIMrFX5hWNR4618Ng1NGK5pswnaS1K8_SrFxDwio=OO5cwh0TYxKrHk7C0DiMckR5_f7AfSahK9xF3CSe3Hw=
>   and 
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>  .
>
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[Freesurfer] Hard failure via XNAT pipeline (Freesurfer 6)

[Rockers, Elijah D.]

We encountered a hard failure, below is the tail of the log. We are currently 
running Freesurfer 6 again locally to see if it succeeds on a desktop machine 
(this is the first time encountering a hard failure on the XNAT server). Any 
suggestions?

  -merging segment 180 into 178
160 defects to be corrected
0 vertices coincident
reading input surface 
/data/build/nnac/20170818_114535/alamode_MRI08162017/20170818114538/alamode_MRI08162017/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
  -face   loglikelihood: -8.7982  (-4.3991)
  -vertex loglikelihood: -6.2982  (-3.1491)
  -normal dot loglikelihood: -3.5611  (-3.5611)
  -quad curv  loglikelihood: -6.1931  (-3.0965)
  Total Loglikelihood : -24.8505

CORRECTING DEFECT 0 (vertices=40706, convex hull=11265, v0=89)
XL defect detected...
Segmentation fault (core dumped)
Linux hhvrixnatp01 2.6.32-431.el6.x86_64 #1 SMP Sun Nov 10 22:19:54 EST 2013 
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s alamode_MRI08162017 exited with ERRORS at Mon Aug 21 19:27:09 CDT 
2017

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


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World Report as the No. 1 hospital in Texas for patient care. Houston Methodist 
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[Freesurfer] Segmentation of WM hypointensities

[Rockers, Elijah D.]

Hello,

The Freesurfer segmentation for hypointensities is very good, but misses on 
some subjects, i.e. it does not include large chunks of hypointense regions in 
some subjects. It does fantastic picking up the periventricular 
hypointensities, but appears to fail on some deep WM regions. I just stumbled 
on an archived message that mentioned an unreleased tool that can use other 
contrasts to improve segmentation.

Is the tool close to being available, by any chance? Or any suggestions for 
improving our segmentations for these?

Many thanks,
- Eli

Houston Methodist. Leading Medicine. U.S. News & World Report has recognized 
Houston Methodist as one of the nation’s top 20 hospitals, placing it for the 
second time on the magazine’s prestigious Honor Roll. It is also designated as 
a Magnet hospital for excellence in nursing.  Visit us at  
houstonmethodist.org. Follow us at  twitter.com/MethodistHosp and 
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[Freesurfer] mri_surf2vol

[Rockers, Elijah D.]

I am attempting to create a volume from a surface. My ultimate goal is to 
obtain a mask that includes everything "inside" the white matter surfaces. 
wm.mgz is close, but it would nicer to just get a mask from lh.white and 
rh.white. I would like these masks to be in the subject's native space. However 
I try the following command and see the resulting error:

mri_surf2vol --o coleMRI06162006/mri/lh.white.mask.mgz --mkmask --hemi lh 
--identity coleMRI06162006 --template coleMRI06162006/mri/orig/orig.mgz

gdiagno = -1
Using identity matrix for registration
mghRead(coleMRI06162006/mri/orig/orig.mgz, -1): could not open file
mri_surf2vol ERROR: reading coleMRI06162006/mri/orig/orig.mgz header

I'm obviously doing something wrong here, but I'm not sure what needs to 
change. I used --identity because native space, and it wouldn't let me run the 
command without specifying --template, which I'm not sure I understand, 
because, again, target is native space. Please illuminate me,

Thank you,

- Eli

Houston Methodist. Leading Medicine. U.S. News & World Report has recognized 
Houston Methodist as one of the nation’s top 20 hospitals, placing it for the 
second time on the magazine’s prestigious Honor Roll. It is also designated as 
a Magnet hospital for excellence in nursing.  Visit us at  
houstonmethodist.org. Follow us at  twitter.com/MethodistHosp and 
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[Freesurfer] mri_glmfit --cortex flag

[Rockers, Elijah D.]

From what I understand, the --cortex flag is simply supposed to zero out any 
signal in the medial wall with a mask, I checked mask.mgh, it is 0 on the 
medial wall and 1 everywhere else as expected... however when I analyze the 
data without this flag, the resulting sig.mgh file has completely changed. 
Areas on the cortex that were "lit up" disappear, and other areas light up that 
were silent before. This should not be happening right?

Houston Methodist. Leading Medicine. U.S. News & World Report has recognized 
Houston Methodist as one of the nation’s top 20 hospitals, placing it for the 
second time on the magazine’s prestigious Honor Roll. It is also designated as 
a Magnet hospital for excellence in nursing.  Visit us at  
houstonmethodist.org. Follow us at  twitter.com/MethodistHosp and 
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[Freesurfer] Qdec input fields

[Rockers, Elijah D.]

Hi,

We like using Qdec to display cortical thickness results. The only drawback is 
that we are unable to manually input values into the boxes for threshold 
values, FDR rate, etc.. We are running Centos7. We thought the graphics drivers 
were the problem, but even after buying a whole new GFX card with different 
drivers, the same problem persists.

Even stranger, our colleague can SSH in from a Mac using X forwarding, and she 
does not experience that problem. I know this may not strictly be a Freesurfer 
problem, but I was hoping someone else may have run into this problem before, 
and has some insight that could help us.

Thanks,
Eli



Houston Methodist. Leading Medicine. U.S. News & World Report has recognized 
Houston Methodist as one of the nation’s top 20 hospitals, placing it for the 
second time on the magazine’s prestigious Honor Roll. It is also designated as 
a Magnet hospital for excellence in nursing.  Visit us at  
houstonmethodist.org. Follow us at  twitter.com/MethodistHosp and 
facebook.com/HoustonMethodist.  ***CONFIDENTIALITY NOTICE*** This e-mail is the 
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restricted and privileged material for the sole use of the intended 
recipient(s). Any review, use, distribution or disclosure by others is strictly 
prohibited. If you are not the intended recipient (or authorized to receive for 
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[Freesurfer] Monte Carlo error (fwhm4 vs. fwhm04)

[Rockers, Elijah D.]

Hello FS,

I am attempting to run a monte carlo simulation on some cortical thickness data 
in Qdec 1.5, but I get the following error:

ERROR: CSDread(): could not open 
../freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm4/abs/th40/mc-z.csd

I thought it might be a permissions issue since the installation is on an NFS 
share, but in fact the  .../lh/cortex/fwhm4/ directory does not exist. 
There is a fwhm04, but not fwhm4. I have two versions of FS installed (5.3 and 
6) so I thought it might be referencing the wrong version, but in fact both 
versions have the same directory structure anyway... Any ideas what is going on?

Thanks,
- Eli

Houston Methodist. Leading Medicine. U.S. News & World Report has recognized 
Houston Methodist as one of the nation’s top 20 hospitals, placing it for the 
second time on the magazine’s prestigious Honor Roll. It is also designated as 
a Magnet hospital for excellence in nursing.  Visit us at  
houstonmethodist.org. Follow us at  twitter.com/MethodistHosp and 
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[Freesurfer] white matter disease

[Rockers, Elijah D.]

Hello,

We have a large number of subjects processed with the default settings of 
recon-all. Unfortunately the presence of white matter creates problems when 
creating the white matter surface. There are large hypo-intensities in the 
white matter which badly distort the surfaces in multiple areas of the brain. 
It is unfortunate because these areas seem to have about the same signal 
intensity as true cortex, leading to a confused algorithm, and very pronounced 
segmentation errors.

I have been manually editing and reconstructing these surfaces, but the process 
is tedious and error prone. Are there any flags that might help recon-all 
perform better on brains with white matter pathology? Or otherwise things that 
I can do to make fixing the segmentation less painful?

Thanks,
Eli

Houston Methodist. Leading Medicine. U.S. News & World Report has recognized 
Houston Methodist as one of the nation’s top 20 hospitals, placing it for the 
second time on the magazine’s prestigious Honor Roll. It is also designated as 
a Magnet hospital for excellence in nursing.  Visit us at  
houstonmethodist.org. Follow us at  twitter.com/MethodistHosp and 
facebook.com/HoustonMethodist.  ***CONFIDENTIALITY NOTICE*** This e-mail is the 
property of Houston Methodist and/or its relevant affiliates and may contain 
restricted and privileged material for the sole use of the intended 
recipient(s). Any review, use, distribution or disclosure by others is strictly 
prohibited. If you are not the intended recipient (or authorized to receive for 
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[Freesurfer] wm.mgz manual editing, revisited

[Rockers, Elijah D.]

Hello all,

Again, I tried to modify the white matter surface by adding voxels to
the wm.mgz file, and performed the reconstruction by doing the
following.

-Opened brainmask.mgz for reference
-Opened wm.mgz on top of that
-Click the voxel edit button
-Check the recon editing checkbox
-Fill in voxels where I want to extend the whitematter surface
-Save wm.mgz
-At terminal, from the appropriate subject directory, run:
recon-all -autorecon2-wm -autorecon3 -subjid my_subject -sd `pwd`

Once this is finished, I examine the surfaces, but they have not
changed. lh/rh.white should be changed to include the voxels I painted
in, correct? 

I have no problem removing voxels from the pial surface, but extending
the white matter is for some reason not working for me, so I am really
stumped as to why these wm.mgz edits aren't making any difference.

Any help with this is vastly appreciated. I have tried this several
times on different subjects with no luck.

Here are links to some relevant files.
001.mgz:
https://1drv.ms/u/s!AoOsIIayCH7qlxLBNvCT4JCvM1Kc

recon-all.logs.tar.gz:
https://1drv.ms/u/s!AoOsIIayCH7qlxRGOWpUCttk5Zji

brainmask+surf+wm.tar.gz
https://1drv.ms/u/s!AoOsIIayCH7qlxbDSS54gfHkq2M3

Thanks,
Eli

Houston Methodist. Leading Medicine.

U.S. News & World Report has recognized Houston Methodist as one of the 
nation’s top 20 hospitals, placing it for the second time on the magazine’s 
prestigious Honor Roll. It is also designated as a Magnet hospital for 
excellence in nursing. Visit us at houstonmethodist.org. Follow us at 
twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist.

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Re: [Freesurfer] wm.mgz manual editing

[Rockers, Elijah D.]

Bruce,

Main problem area that I can see is at coordinates [104,42,124].

My first attempt, I don't think I had the recon editing box checked when
I was editing the white matter, but I used a brush value of 255. My
second attempt I painted over the same voxels but with the recon editing
box checked.

Both times, after saving wm.mgz I ran the following command:
"recon-all -autorecon2-wm -autorecon3 -subjid my_subject -sd `pwd`"
Only thing different from the guide is I specify a different subject
directory.

Below are download links for the important files, let me know if you
would like to look at anything else. If you look at wm.mgz along with
the rh.white, you can see the surface doesn't appear to acknowledge my
edit.

001.mgz:
https://1drv.ms/u/s!AoOsIIayCH7qlxLBNvCT4JCvM1Kc

recon-all.logs.tar.gz:
https://1drv.ms/u/s!AoOsIIayCH7qlxRGOWpUCttk5Zji

brainmask+surf+wm.tar.gz
https://1drv.ms/u/s!AoOsIIayCH7qlxbDSS54gfHkq2M3

Thanks tremendously for your time,
Eli

> --
> 
> Message: 4
> Date: Wed, 1 Mar 2017 16:39:33 -0500 (EST)
> From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] wm.mgz manual editing
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Message-ID:
>   
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__alpine.LRH.2.20.1703011638420.14038-40door.nmr.mgh.harvard.edu=DwICAg=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q=yBgXIybzSgTt6ZfKp6pNzp_N8aWytMgQmmsZVDx1AwI=BM5wWGqXMNLiptKsXqsKDinkU3EtRMoCYFuj0Gbx650=
>  >
> Content-Type: text/plain; charset="utf-8"
> 
> Hi Eli
> 
> hmm, maybe you should just upload the subject and email us the voxel 
> coords you are talking about?
> 
> Also, in general it is hard for us to help you unless you include more 
> information. What exact command did you run? What was the screen output? 
> What was in the recon-all.log?
> 
> cheers
> Bruce
> 
> 
> On Wed, 1 
> Mar 2017, Rockers, Elijah D. wrote:
> 
> > Couple of questions:
> >
> > 1)
> >
> > I edited wm.mgz following the instructions in the wiki guide, but it did
> > not change anything after reconstruction. I am still using 5.3 right
> > now, so maybe the guide is wrong for me. What is the brush value
> > supposed to be? I used 255 but it did not extend the white matter
> > surface to include my edits. I checked to make sure they saved
> > correctly, they did, but the surface didn't change. Any ideas?
> >
> > 2)
> >
> > The reason I am editing wm.mgz is to try to include some cortex that was
> > left out of the pial surface. I don't suppose there's any way to fix
> > this without editing wm.mgz? Because the white matter surface actually
> > looks fine the way it is.
> >
> > Thanks,
> > Eli
> >
> > Houston Methodist. Leading Medicine.
> >



Houston Methodist. Leading Medicine.

U.S. News & World Report has recognized Houston Methodist as one of the 
nation’s top 20 hospitals, placing it for the second time on the magazine’s 
prestigious Honor Roll. It is also designated as a Magnet hospital for 
excellence in nursing. Visit us at houstonmethodist.org. Follow us at 
twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist.

***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist 
Hospital and/or its relevant affiliates and may contain restricted and 
privileged material for the sole use of the intended recipient(s). Any review, 
use, distribution or disclosure by others is strictly prohibited. If you are 
not the intended recipient (or authorized to receive for the recipient), please 
contact the sender and delete all copies of the message. Thank you.

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Re: [Freesurfer] wm.mgz manual editing

[Rockers, Elijah D.]

Bruce,

Main problem area that I can see is at coordinates [104,42,124].

My first attempt, I don't think I had the recon editing box checked when
I was editing the white matter, but I used a brush value of 255. My
second attempt I painted over the same voxels but with the recon editing
box checked.

Both times, after saving wm.mgz I ran the following command:
"recon-all -autorecon2-wm -autorecon3 -subjid my_subject -sd `pwd`"
Only thing different from the guide is I specify a different subject
directory.

Below are download links for the important files, let me know if you
would like to look at anything else. If you look at wm.mgz along with
the rh.white, you can see the surface doesn't appear to acknowledge my
edit.

001.mgz:
https://1drv.ms/u/s!AoOsIIayCH7qlxLBNvCT4JCvM1Kc

recon-all.logs.tar.gz:
https://1drv.ms/u/s!AoOsIIayCH7qlxRGOWpUCttk5Zji

brainmask+surf+wm.tar.gz
https://1drv.ms/u/s!AoOsIIayCH7qlxbDSS54gfHkq2M3

Thanks tremendously for your time,
Eli

> --
> 
> Message: 4
> Date: Wed, 1 Mar 2017 16:39:33 -0500 (EST)
> From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] wm.mgz manual editing
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Message-ID:
>   
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__alpine.LRH.2.20.1703011638420.14038-40door.nmr.mgh.harvard.edu=DwICAg=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q=yBgXIybzSgTt6ZfKp6pNzp_N8aWytMgQmmsZVDx1AwI=BM5wWGqXMNLiptKsXqsKDinkU3EtRMoCYFuj0Gbx650=
>  >
> Content-Type: text/plain; charset="utf-8"
> 
> Hi Eli
> 
> hmm, maybe you should just upload the subject and email us the voxel 
> coords you are talking about?
> 
> Also, in general it is hard for us to help you unless you include more 
> information. What exact command did you run? What was the screen output? 
> What was in the recon-all.log?
> 
> cheers
> Bruce
> 
> 
> On Wed, 1 
> Mar 2017, Rockers, Elijah D. wrote:
> 
> > Couple of questions:
> >
> > 1)
> >
> > I edited wm.mgz following the instructions in the wiki guide, but it did
> > not change anything after reconstruction. I am still using 5.3 right
> > now, so maybe the guide is wrong for me. What is the brush value
> > supposed to be? I used 255 but it did not extend the white matter
> > surface to include my edits. I checked to make sure they saved
> > correctly, they did, but the surface didn't change. Any ideas?
> >
> > 2)
> >
> > The reason I am editing wm.mgz is to try to include some cortex that was
> > left out of the pial surface. I don't suppose there's any way to fix
> > this without editing wm.mgz? Because the white matter surface actually
> > looks fine the way it is.
> >
> > Thanks,
> > Eli
> >
> > Houston Methodist. Leading Medicine.
> >


Houston Methodist. Leading Medicine.

U.S. News & World Report has recognized Houston Methodist as one of the 
nation’s top 20 hospitals, placing it for the second time on the magazine’s 
prestigious Honor Roll. It is also designated as a Magnet hospital for 
excellence in nursing. Visit us at houstonmethodist.org. Follow us at 
twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist.

***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist 
Hospital and/or its relevant affiliates and may contain restricted and 
privileged material for the sole use of the intended recipient(s). Any review, 
use, distribution or disclosure by others is strictly prohibited. If you are 
not the intended recipient (or authorized to receive for the recipient), please 
contact the sender and delete all copies of the message. Thank you.

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[Freesurfer] wm.mgz manual editing

[Rockers, Elijah D.]

Couple of questions:

1)

I edited wm.mgz following the instructions in the wiki guide, but it did
not change anything after reconstruction. I am still using 5.3 right
now, so maybe the guide is wrong for me. What is the brush value
supposed to be? I used 255 but it did not extend the white matter
surface to include my edits. I checked to make sure they saved
correctly, they did, but the surface didn't change. Any ideas?

2)

The reason I am editing wm.mgz is to try to include some cortex that was
left out of the pial surface. I don't suppose there's any way to fix
this without editing wm.mgz? Because the white matter surface actually
looks fine the way it is.

Thanks,
Eli

Houston Methodist. Leading Medicine.

U.S. News & World Report has recognized Houston Methodist as one of the 
nation’s top 20 hospitals, placing it for the second time on the magazine’s 
prestigious Honor Roll. It is also designated as a Magnet hospital for 
excellence in nursing. Visit us at houstonmethodist.org. Follow us at 
twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist.

***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist 
Hospital and/or its relevant affiliates and may contain restricted and 
privileged material for the sole use of the intended recipient(s). Any review, 
use, distribution or disclosure by others is strictly prohibited. If you are 
not the intended recipient (or authorized to receive for the recipient), please 
contact the sender and delete all copies of the message. Thank you.

___
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Re: [Freesurfer] Manual edit to include missing cortex?

[Rockers, Elijah D.]

I edited the wm.mgz according to the guide, but it didn't change
anything when I ran the reconstruction.

What is the brush value supposed to be when editing? 255?

On Tue, 2017-02-28 at 08:33 -0500,
freesurfer-requ...@nmr.mgh.harvard.edu wrote:
> Send Freesurfer mailing list submissions to
>   freesurfer@nmr.mgh.harvard.edu
> 
> To subscribe or unsubscribe via the World Wide Web, visit
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>  
> or, via email, send a message with subject or body 'help' to
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> 
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> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Freesurfer digest..."
> 
> 
> Today's Topics:
> 
>1. Manual edit to include missing cortex? (Rockers, Elijah D.)
>2. Re: Manual edit to include missing cortex? (Lee Tirrell)
>3. How to output particular area from stats subdir (Jing Gu)
>4. Re: chose between 5.3 and 6.0 (Bruce Fischl)
>5. Ct file (yusif Al-kheder)
>6. Re: Ct file (Douglas N Greve)
>7. Different segmentation atlas (Julie Hall)
>8. Re: gzip: stdin: unexpected end of file (Kambiz Tavabi)
>9. Re: gzip: stdin: unexpected end of file
>   (zkauf...@nmr.mgh.harvard.edu)
>   10. Building Freesurfer dev with GPU support/CUDA enabled
>   (Francis Tyson Thomas)
>   11. ACPC alignment before or after running on Freesurfer?
>   (Lee Subin Kristine)
>   12. Re: ACPC alignment before or after running on Freesurfer?
>   (Antonin Skoch)
>   13. Re: Strange wm error (Melanie Ganz)
>   14. Re: Building Freesurfer dev with GPU support/CUDA   enabled
>   (R Edgar)
>   15. Re: XL defect detected (Shane S)
>   16. Re: editing topological defect (Shane S)
>   17. Re: chose between 5.3 and 6.0 (Shane S)
>   18. mri_convert error: 'GetDICOMInfo(): dcmGetDWIParams()   7' in
>   FS6.0 (Gustav M?rtensson)
> 
> 
> ------
> 
> Message: 1
> Date: Mon, 27 Feb 2017 21:45:39 +
> From: "Rockers, Elijah D." <edrock...@houstonmethodist.org>
> Subject: [Freesurfer] Manual edit to include missing cortex?
> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <1488231939.3484.60.ca...@houstonmethodist.org>
> Content-Type: text/plain; charset="utf-8"
> 
> Is there something I can do to extend the pial surface to include cortex
> that it ignored? In some places there are rather large chunks of cortex
> not included in the pial surface.
> 
> https://urldefense.proofpoint.com/v2/url?u=http-3A__imgur.com_a_FnAgj=DwICAg=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q=b6w_71LvjLBcrHSvh9GBgb0eynsUY9n9xd3ZMU-AVEU=bUoYvwIUVPBh2GqxxJBmM5PPMRasPMoCnG44Zr233L8=
>  
> 
> Link is to a screenshot, notice the top of the brain. It's fairly
> pronounced, visible in 12 adjacent sagittal slices.
> 
> I tried using the "Reposition Surface" tool, but I'm not exactly how it
> works, and I ended up just making the surface look crazy there.
> 
> I also tried adding control points in the white matter near the edges of
> the WM surface by the problem and ran the reconstruction, as someone in
> the archives suggested, but it didn't change the surface.
> 
> Thanks for your help,
> Eli
> 
> Houston Methodist. Leading Medicine.
> 
> U.S. News & World Report has recognized Houston Methodist as one of the 
> nation?s top 20 hospitals, placing it for the second time on the magazine?s 
> prestigious Honor Roll. It is also designated as a Magnet hospital for 
> excellence in nursing. Visit us at houstonmethodist.org. Follow us at 
> https://urldefense.proofpoint.com/v2/url?u=http-3A__twitter.com_MethodistHosp=DwICAg=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q=b6w_71LvjLBcrHSvh9GBgb0eynsUY9n9xd3ZMU-AVEU=tdm1uCFp1Qa-cqbw-ETWTqnNcjd9OmsdyD2Fx1Z7tzQ=
>   and 
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.facebook.com_HoustonMethodist=DwICAg=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q=b6w_71LvjLBcrHSvh9GBgb0eynsUY9n9xd3ZMU-AVEU=7GrzKHkkWqTKw3HTTh9lCXDMVPdu9qlbNLMf4MiQXz4=
>  .
> 
> ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist 
> Hospital and/or its relevant affiliates and may cont

[Freesurfer] Freeview default cursor

[Rockers, Elijah D.]

Hello,

I could not find any information on changing the cursor via command
line. My goal is to persistently change the default cursor style/color,
I was going to create an alias on my system.

Thanks,
Eli

Houston Methodist. Leading Medicine.

U.S. News & World Report has recognized Houston Methodist as one of the 
nation’s top 20 hospitals, placing it for the second time on the magazine’s 
prestigious Honor Roll. It is also designated as a Magnet hospital for 
excellence in nursing. Visit us at houstonmethodist.org. Follow us at 
twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist.

***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist 
Hospital and/or its relevant affiliates and may contain restricted and 
privileged material for the sole use of the intended recipient(s). Any review, 
use, distribution or disclosure by others is strictly prohibited. If you are 
not the intended recipient (or authorized to receive for the recipient), please 
contact the sender and delete all copies of the message. Thank you.

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[Freesurfer] Manual edit to include missing cortex?

[Rockers, Elijah D.]

Is there something I can do to extend the pial surface to include cortex
that it ignored? In some places there are rather large chunks of cortex
not included in the pial surface.

http://imgur.com/a/FnAgj

Link is to a screenshot, notice the top of the brain. It's fairly
pronounced, visible in 12 adjacent sagittal slices.

I tried using the "Reposition Surface" tool, but I'm not exactly how it
works, and I ended up just making the surface look crazy there.

I also tried adding control points in the white matter near the edges of
the WM surface by the problem and ran the reconstruction, as someone in
the archives suggested, but it didn't change the surface.

Thanks for your help,
Eli

Houston Methodist. Leading Medicine.

U.S. News & World Report has recognized Houston Methodist as one of the 
nation’s top 20 hospitals, placing it for the second time on the magazine’s 
prestigious Honor Roll. It is also designated as a Magnet hospital for 
excellence in nursing. Visit us at houstonmethodist.org. Follow us at 
twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist.

***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist 
Hospital and/or its relevant affiliates and may contain restricted and 
privileged material for the sole use of the intended recipient(s). Any review, 
use, distribution or disclosure by others is strictly prohibited. If you are 
not the intended recipient (or authorized to receive for the recipient), please 
contact the sender and delete all copies of the message. Thank you.

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Re: [Freesurfer] Disastrous Soft Error

[Rockers, Elijah D.]

OK, sorry for spamming the list. I fixed the the faulty skullstrip by using

recon-all -skullstrip -clean-bm -no-wsgcaatlas -subjid 

Currently redoing the surface reconstructions, but it should be OK now.
Thanks for the nice documentation.
Eli


On Fri, 2017-02-24 at 15:30 -0600, Elijah Rockers wrote:


As far as I can tell, everything looks OK up until brainmask.mgz. The
skullstrip step seems to have cropped out the brain and left the neck...

On Fri, 2017-02-24 at 12:58 -0600, Elijah Rockers wrote:
> Hello all,
>
> I recon-all'd ~40 different subjects. I have been going through all the
> images to make sure they were processed correctly. Most required no no
> editing and recon-all did a very good job.
>
> But for one scan in particular, it looks like Freesurfer thinks the top
> of the spinal cord is the brain. Several vertebrae are very nicely
> segmented... :P
>
> Just wondering if you have any suggestions for reprocessing this
> subject? The error is reproducible with default recon-all settings.
>
> Subject has some pathology in the white matter which might be causing
> the problem?
>
> Screenshot of T1.mgz + lh.pial at the following link:
> http://imgur.com/a/uwyaq
>
> Thanks,
> Eli




Houston Methodist. Leading Medicine. U.S. News & World Report has recognized 
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Re: [Freesurfer] Disastrous Soft Error

[Rockers, Elijah D.]

As far as I can tell, everything looks OK up until brainmask.mgz. The
skullstrip step seems to have cropped out the brain and left the neck...

On Fri, 2017-02-24 at 12:58 -0600, Elijah Rockers wrote:
> Hello all,
> 
> I recon-all'd ~40 different subjects. I have been going through all the
> images to make sure they were processed correctly. Most required no no
> editing and recon-all did a very good job.
> 
> But for one scan in particular, it looks like Freesurfer thinks the top
> of the spinal cord is the brain. Several vertebrae are very nicely
> segmented... :P
> 
> Just wondering if you have any suggestions for reprocessing this
> subject? The error is reproducible with default recon-all settings.
> 
> Subject has some pathology in the white matter which might be causing
> the problem?
> 
> Screenshot of T1.mgz + lh.pial at the following link:
> http://imgur.com/a/uwyaq
> 
> Thanks,
> Eli


Houston Methodist. Leading Medicine.

U.S. News & World Report has recognized Houston Methodist as one of the 
nation’s top 20 hospitals, placing it for the second time on the magazine’s 
prestigious Honor Roll. It is also designated as a Magnet hospital for 
excellence in nursing. Visit us at houstonmethodist.org. Follow us at 
twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist.

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[Freesurfer] Disastrous Soft Error

[Rockers, Elijah D.]

Hello all,

I recon-all'd ~40 different subjects. I have been going through all the
images to make sure they were processed correctly. Most required no no
editing and recon-all did a very good job.

But for one scan in particular, it looks like Freesurfer thinks the top
of the spinal cord is the brain. Several vertebrae are very nicely
segmented... :P

Just wondering if you have any suggestions for reprocessing this
subject? The error is reproducible with default recon-all settings.

Subject has some pathology in the white matter which might be causing
the problem?

Screenshot of T1.mgz + lh.pial at the following link:
http://imgur.com/a/uwyaq

Thanks,
Eli

Houston Methodist. Leading Medicine.

U.S. News & World Report has recognized Houston Methodist as one of the 
nation’s top 20 hospitals, placing it for the second time on the magazine’s 
prestigious Honor Roll. It is also designated as a Magnet hospital for 
excellence in nursing. Visit us at houstonmethodist.org. Follow us at 
twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist.

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Hospital and/or its relevant affiliates and may contain restricted and 
privileged material for the sole use of the intended recipient(s). Any review, 
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Re: [Freesurfer] No FTP Access

[Rockers, Elijah D.]

Nevermind. I discovered if I just change ftp to https in the download
link, it works fine.
- Eli

On Wed, 2017-02-22 at 12:22 -0500, Elijah Rockers wrote:
> Is there by any chance another way to download Freesurfer? My
> institution does not allow FTP connections (HIPPA...) Same goes for the
> tutorial data, but obviously Freesurfer is the priority here... thanks.
> 
> - Eli


Houston Methodist. Leading Medicine.

U.S. News & World Report has recognized Houston Methodist as one of the 
nation’s top 20 hospitals, placing it for the second time on the magazine’s 
prestigious Honor Roll. It is also designated as a Magnet hospital for 
excellence in nursing. Visit us at houstonmethodist.org. Follow us at 
twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist.

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[Freesurfer] No FTP Access

[Rockers, Elijah D.]

Is there by any chance another way to download Freesurfer? My
institution does not allow FTP connections (HIPPA...) Same goes for the
tutorial data, but obviously Freesurfer is the priority here... thanks.

- Eli

Houston Methodist. Leading Medicine.

U.S. News & World Report has recognized Houston Methodist as one of the 
nation’s top 20 hospitals, placing it for the second time on the magazine’s 
prestigious Honor Roll. It is also designated as a Magnet hospital for 
excellence in nursing. Visit us at houstonmethodist.org. Follow us at 
twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist.

***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist 
Hospital and/or its relevant affiliates and may contain restricted and 
privileged material for the sole use of the intended recipient(s). Any review, 
use, distribution or disclosure by others is strictly prohibited. If you are 
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contact the sender and delete all copies of the message. Thank you.

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Re: [Freesurfer] mri_convert slope scale

[Rockers, Elijah D.]

Yes, (2005,100d) is the philips MRI intercept tag. it is zero in all of 
our scans unfortunately they are using private tags for philips MR. 
the 28,1052/1053 are the public tags, which their PET thankfully uses... 
but for the MR they are empty.

I'm using bash, so i did export FS_SLICE_LIN_SCALE=1, but there was no 
change in the output, still only seeing raw DICOM values. (also, slope 
scale did not copy into the header, either behavior would be desireable)

One more thing, the slope scale for Philips MRI, 2005,100e is actually 
an inverse slope scale, i.e., for accurate quantitative analysis, the 
images must be divided by the value in the slope scale header we are 
under the impression this is an issue unique to Philips MRI images. See 
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3998685/ for more info.


On 11/18/2016 10:37 AM, Douglas N Greve wrote:
> Try converting the PET after setting this env var
>
> setenv FS_SLICE_LIN_SCALE 1
>
> This causes mri_convert to read 28,1052 (intercept) and 28,1053 
> (slope). the output value should be
>
> dicomvalue*slope + intercept
>
> Is 2005,100e accompanied by an intercept ?
>
>
>
> On 11/18/2016 11:25 AM, Rockers, Elijah D. wrote:
>> Doug,
>>
>> Any update on this?
>>
>> Thanks,
>> Eli
>>
>> On 11/10/2016 12:52 PM, Eli wrote:
>>> (2005,100e) for MRI (Philips)
>>> (0028,1053) for PET (Philips)
>>>
>>> I understand the PET may not be intended to work, but it doesn't seem
>>> to be copying over or applying the scale for either modality.
>>>
>>> On 11/10/2016 12:40 PM, Douglas N Greve wrote:
>>>> What is the dicom tag for the scale?
>>>>
>>>>
>>>> On 11/10/2016 01:29 PM, Rockers, Elijah D. wrote:
>>>>> As far as I can tell, mri_convert doesn't apply the scaling 
>>>>> factor, and
>>>>> also doesn't copy over the slope scale header entry, when converting
>>>>> from dicom to nifti.
>>>>>
>>>>> By contrast, dcm2nii does not apply the scale either, however, it
>>>>> copies
>>>>> over the slope scale header entry, enabling other software (eg
>>>>> Freeview..) to apply the scaling..
>>>>>
>>>>> Hope this clarifies. Thanks for checking into this.
>>>>>
>>>>> On 11/10/2016 12:18 PM, Douglas N Greve wrote:
>>>>>> Sorry, is it a scale in the dicom file or the nifti file that is not
>>>>>> being applied properly?
>>>>>>
>>>>>>
>>>>>> On 11/10/2016 11:01 AM, Rockers, Elijah D. wrote:
>>>>>>> Doug,
>>>>>>>
>>>>>>> Can you verify? The dicom and mri_covnert .nii are identical 
>>>>>>> (integer
>>>>>>> values, as per dicom convention) when we inspect the matrix in
>>>>>>> MATLAB.
>>>>>>>
>>>>>>> The img matrices for mri_convert and dcm2nii are also identical, 
>>>>>>> the
>>>>>>> difference appears to be that dcm2nii retains the slope scale in 
>>>>>>> the
>>>>>>> header, allowing the viewer (freeview, pmod, etc..) to apply it.
>>>>>>>
>>>>>>> We have been trying to nail down this issue for the last couple 
>>>>>>> days,
>>>>>>> any insight would be appreciated.
>>>>>>>
>>>>>>> Eli
>>>>>>>
>>>>>>> On 11/09/2016 05:51 PM, freesurfer-requ...@nmr.mgh.harvard.edu 
>>>>>>> wrote:
>>>>>>>> Message: 2 Date: Wed, 9 Nov 2016 16:01:18 -0500 From: Douglas N
>>>>>>>> Greve
>>>>>>>> <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_convert
>>>>>>>> slope scale To: freesurfer@nmr.mgh.harvard.edu Message-ID:
>>>>>>>> <908818ac-156f-f6d2-1338-694626cde...@nmr.mgh.harvard.edu>
>>>>>>>> Content-Type: text/plain; charset=utf-8; format=flowed I think we
>>>>>>>> actually apply the scaling, so including it in the output would be
>>>>>>>> inappropriate. On 11/09/2016 03:03 PM, Rockers, Elijah D. wrote:
>>>>>>>>>> Hello,
>>>>>>>>>>
>>>>>>>>>> We have been using mri_convert to convert our dicoms into .nii
>>>>>>>>>> niftis.
>>>>>>>

Re: [Freesurfer] mri_convert slope scale

[Rockers, Elijah D.]

Doug,

Any update on this?

Thanks,
Eli

On 11/10/2016 12:52 PM, Eli wrote:
> (2005,100e) for MRI (Philips)
> (0028,1053) for PET (Philips)
>
> I understand the PET may not be intended to work, but it doesn't seem 
> to be copying over or applying the scale for either modality.
>
> On 11/10/2016 12:40 PM, Douglas N Greve wrote:
>> What is the dicom tag for the scale?
>>
>>
>> On 11/10/2016 01:29 PM, Rockers, Elijah D. wrote:
>>> As far as I can tell, mri_convert doesn't apply the scaling factor, and
>>> also doesn't copy over the slope scale header entry, when converting
>>> from dicom to nifti.
>>>
>>> By contrast, dcm2nii does not apply the scale either, however, it 
>>> copies
>>> over the slope scale header entry, enabling other software (eg
>>> Freeview..) to apply the scaling..
>>>
>>> Hope this clarifies. Thanks for checking into this.
>>>
>>> On 11/10/2016 12:18 PM, Douglas N Greve wrote:
>>>> Sorry, is it a scale in the dicom file or the nifti file that is not
>>>> being applied properly?
>>>>
>>>>
>>>> On 11/10/2016 11:01 AM, Rockers, Elijah D. wrote:
>>>>> Doug,
>>>>>
>>>>> Can you verify? The dicom and mri_covnert .nii are identical (integer
>>>>> values, as per dicom convention) when we inspect the matrix in 
>>>>> MATLAB.
>>>>>
>>>>> The img matrices for mri_convert and dcm2nii are also identical, the
>>>>> difference appears to be that dcm2nii retains the slope scale in the
>>>>> header, allowing the viewer (freeview, pmod, etc..) to apply it.
>>>>>
>>>>> We have been trying to nail down this issue for the last couple days,
>>>>> any insight would be appreciated.
>>>>>
>>>>> Eli
>>>>>
>>>>> On 11/09/2016 05:51 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
>>>>>> Message: 2 Date: Wed, 9 Nov 2016 16:01:18 -0500 From: Douglas N 
>>>>>> Greve
>>>>>> <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_convert
>>>>>> slope scale To: freesurfer@nmr.mgh.harvard.edu Message-ID:
>>>>>> <908818ac-156f-f6d2-1338-694626cde...@nmr.mgh.harvard.edu>
>>>>>> Content-Type: text/plain; charset=utf-8; format=flowed I think we
>>>>>> actually apply the scaling, so including it in the output would be
>>>>>> inappropriate. On 11/09/2016 03:03 PM, Rockers, Elijah D. wrote:
>>>>>>>> Hello,
>>>>>>>>
>>>>>>>> We have been using mri_convert to convert our dicoms into .nii
>>>>>>>> niftis.
>>>>>>>> There is an entry in the .nii header for the slope scale, but
>>>>>>>> mri_convert appears to discard this value instead of copying it
>>>>>>>> into the
>>>>>>>> header (whereas mricron retains this value) We prefer to use
>>>>>>>> mri_convert.
>>>>>>>>
>>>>>>>> Is there a way to have mri_convert carry this value over? Why 
>>>>>>>> is it
>>>>>>>> being discarded?
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Eli
>>>>>>>>
>>
>

-- 
Elijah Rockers
Research Data Analyst
Houston Methodist Research Institute
O: 713-363-7729

Houston Methodist. Leading Medicine.

U.S. News & World Report has recognized Houston Methodist as one of the 
nation’s top 20 hospitals, placing it for the second time on the magazine’s 
prestigious Honor Roll. It is also designated as a Magnet hospital for 
excellence in nursing. Visit us at houstonmethodist.org. Follow us at 
twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist.

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Re: [Freesurfer] mri_convert slope scale

[Rockers, Elijah D.]

(2005,100e) for MRI (Philips)
(0028,1053) for PET (Philips)

I understand the PET may not be intended to work, but it doesn't seem to 
be copying over or applying the scale for either modality.

On 11/10/2016 12:40 PM, Douglas N Greve wrote:
> What is the dicom tag for the scale?
>
>
> On 11/10/2016 01:29 PM, Rockers, Elijah D. wrote:
>> As far as I can tell, mri_convert doesn't apply the scaling factor, and
>> also doesn't copy over the slope scale header entry, when converting
>> from dicom to nifti.
>>
>> By contrast, dcm2nii does not apply the scale either, however, it copies
>> over the slope scale header entry, enabling other software (eg
>> Freeview..) to apply the scaling..
>>
>> Hope this clarifies. Thanks for checking into this.
>>
>> On 11/10/2016 12:18 PM, Douglas N Greve wrote:
>>> Sorry, is it a scale in the dicom file or the nifti file that is not
>>> being applied properly?
>>>
>>>
>>> On 11/10/2016 11:01 AM, Rockers, Elijah D. wrote:
>>>> Doug,
>>>>
>>>> Can you verify? The dicom and mri_covnert .nii are identical (integer
>>>> values, as per dicom convention) when we inspect the matrix in MATLAB.
>>>>
>>>> The img matrices for mri_convert and dcm2nii are also identical, the
>>>> difference appears to be that dcm2nii retains the slope scale in the
>>>> header, allowing the viewer (freeview, pmod, etc..) to apply it.
>>>>
>>>> We have been trying to nail down this issue for the last couple days,
>>>> any insight would be appreciated.
>>>>
>>>> Eli
>>>>
>>>> On 11/09/2016 05:51 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
>>>>> Message: 2 Date: Wed, 9 Nov 2016 16:01:18 -0500 From: Douglas N Greve
>>>>> <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_convert
>>>>> slope scale To: freesurfer@nmr.mgh.harvard.edu Message-ID:
>>>>> <908818ac-156f-f6d2-1338-694626cde...@nmr.mgh.harvard.edu>
>>>>> Content-Type: text/plain; charset=utf-8; format=flowed I think we
>>>>> actually apply the scaling, so including it in the output would be
>>>>> inappropriate. On 11/09/2016 03:03 PM, Rockers, Elijah D. wrote:
>>>>>>> Hello,
>>>>>>>
>>>>>>> We have been using mri_convert to convert our dicoms into .nii
>>>>>>> niftis.
>>>>>>> There is an entry in the .nii header for the slope scale, but
>>>>>>> mri_convert appears to discard this value instead of copying it
>>>>>>> into the
>>>>>>> header (whereas mricron retains this value) We prefer to use
>>>>>>> mri_convert.
>>>>>>>
>>>>>>> Is there a way to have mri_convert carry this value over? Why is it
>>>>>>> being discarded?
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Eli
>>>>>>>
>

-- 
Elijah Rockers
Research Data Analyst
Houston Methodist Research Institute
O: 713-363-7729

Houston Methodist. Leading Medicine.

U.S. News & World Report has recognized Houston Methodist as one of the 
nation’s top 20 hospitals, placing it for the second time on the magazine’s 
prestigious Honor Roll. It is also designated as a Magnet hospital for 
excellence in nursing. Visit us at houstonmethodist.org. Follow us at 
twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist.

***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist 
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privileged material for the sole use of the intended recipient(s). Any review, 
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Re: [Freesurfer] mri_convert slope scale

[Rockers, Elijah D.]

As far as I can tell, mri_convert doesn't apply the scaling factor, and 
also doesn't copy over the slope scale header entry, when converting 
from dicom to nifti.

By contrast, dcm2nii does not apply the scale either, however, it copies 
over the slope scale header entry, enabling other software (eg 
Freeview..) to apply the scaling..

Hope this clarifies. Thanks for checking into this.

On 11/10/2016 12:18 PM, Douglas N Greve wrote:
> Sorry, is it a scale in the dicom file or the nifti file that is not 
> being applied properly?
>
>
> On 11/10/2016 11:01 AM, Rockers, Elijah D. wrote:
>> Doug,
>>
>> Can you verify? The dicom and mri_covnert .nii are identical (integer
>> values, as per dicom convention) when we inspect the matrix in MATLAB.
>>
>> The img matrices for mri_convert and dcm2nii are also identical, the
>> difference appears to be that dcm2nii retains the slope scale in the
>> header, allowing the viewer (freeview, pmod, etc..) to apply it.
>>
>> We have been trying to nail down this issue for the last couple days,
>> any insight would be appreciated.
>>
>> Eli
>>
>> On 11/09/2016 05:51 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
>>> Message: 2 Date: Wed, 9 Nov 2016 16:01:18 -0500 From: Douglas N Greve
>>> <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_convert
>>> slope scale To: freesurfer@nmr.mgh.harvard.edu Message-ID:
>>> <908818ac-156f-f6d2-1338-694626cde...@nmr.mgh.harvard.edu>
>>> Content-Type: text/plain; charset=utf-8; format=flowed I think we
>>> actually apply the scaling, so including it in the output would be
>>> inappropriate. On 11/09/2016 03:03 PM, Rockers, Elijah D. wrote:
>>>>> Hello,
>>>>>
>>>>> We have been using mri_convert to convert our dicoms into .nii 
>>>>> niftis.
>>>>> There is an entry in the .nii header for the slope scale, but
>>>>> mri_convert appears to discard this value instead of copying it 
>>>>> into the
>>>>> header (whereas mricron retains this value) We prefer to use 
>>>>> mri_convert.
>>>>>
>>>>> Is there a way to have mri_convert carry this value over? Why is it
>>>>> being discarded?
>>>>>
>>>>> Thanks,
>>>>> Eli
>>>>>
>

-- 
Elijah Rockers
Research Data Analyst
Houston Methodist Research Institute
O: 713-363-7729

Houston Methodist. Leading Medicine.

U.S. News & World Report has recognized Houston Methodist as one of the 
nation’s top 20 hospitals, placing it for the second time on the magazine’s 
prestigious Honor Roll. It is also designated as a Magnet hospital for 
excellence in nursing. Visit us at houstonmethodist.org. Follow us at 
twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist.

***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist 
Hospital and/or its relevant affiliates and may contain restricted and 
privileged material for the sole use of the intended recipient(s). Any review, 
use, distribution or disclosure by others is strictly prohibited. If you are 
not the intended recipient (or authorized to receive for the recipient), please 
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Re: [Freesurfer] mri_convert slope scale

[Rockers, Elijah D.]

Doug,

Can you verify? The dicom and mri_covnert .nii are identical (integer 
values, as per dicom convention) when we inspect the matrix in MATLAB.

The img matrices for mri_convert and dcm2nii are also identical, the 
difference appears to be that dcm2nii retains the slope scale in the 
header, allowing the viewer (freeview, pmod, etc..) to apply it.

We have been trying to nail down this issue for the last couple days, 
any insight would be appreciated.

Eli

On 11/09/2016 05:51 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
> Message: 2 Date: Wed, 9 Nov 2016 16:01:18 -0500 From: Douglas N Greve 
> <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_convert 
> slope scale To: freesurfer@nmr.mgh.harvard.edu Message-ID: 
> <908818ac-156f-f6d2-1338-694626cde...@nmr.mgh.harvard.edu> 
> Content-Type: text/plain; charset=utf-8; format=flowed I think we 
> actually apply the scaling, so including it in the output would be 
> inappropriate. On 11/09/2016 03:03 PM, Rockers, Elijah D. wrote:
>> >Hello,
>> >
>> >We have been using mri_convert to convert our dicoms into .nii niftis.
>> >There is an entry in the .nii header for the slope scale, but
>> >mri_convert appears to discard this value instead of copying it into the
>> >header (whereas mricron retains this value) We prefer to use mri_convert.
>> >
>> >Is there a way to have mri_convert carry this value over? Why is it
>> >being discarded?
>> >
>> >Thanks,
>> >Eli
>> >

-- 
Elijah Rockers
Research Data Analyst
Houston Methodist Research Institute
O: 713-363-7729

Houston Methodist. Leading Medicine.

U.S. News & World Report has recognized Houston Methodist as one of the 
nation’s top 20 hospitals, placing it for the second time on the magazine’s 
prestigious Honor Roll. It is also designated as a Magnet hospital for 
excellence in nursing. Visit us at houstonmethodist.org. Follow us at 
twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist.

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[Freesurfer] mri_convert slope scale

[Rockers, Elijah D.]

Hello,

We have been using mri_convert to convert our dicoms into .nii niftis. 
There is an entry in the .nii header for the slope scale, but 
mri_convert appears to discard this value instead of copying it into the 
header (whereas mricron retains this value) We prefer to use mri_convert.

Is there a way to have mri_convert carry this value over? Why is it 
being discarded?

Thanks,
Eli

Houston Methodist. Leading Medicine.

U.S. News & World Report has recognized Houston Methodist as one of the 
nation’s top 20 hospitals, placing it for the second time on the magazine’s 
prestigious Honor Roll. It is also designated as a Magnet hospital for 
excellence in nursing. Visit us at houstonmethodist.org. Follow us at 
twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist.

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[Freesurfer] S. Nigra

[Rockers, Elijah D.]

Is it possible for freesurfer to parcellate the substantia nigra from a T1?

-- 
Elijah Rockers
Research Data Analyst
Houston Methodist Research Institute
O: 713-363-7729

Houston Methodist. Leading Medicine.

U.S. News & World Report has recognized Houston Methodist as one of the 
nation’s top 20 hospitals, placing it for the second time on the magazine’s 
prestigious Honor Roll. It is also designated as a Magnet hospital for 
excellence in nursing. Visit us at houstonmethodist.org. Follow us at 
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[Freesurfer] recon-all warnings

[Rockers, Elijah D.]

Hello,

Doing a recon-all -all yields some deprecation warnings.

defined(@array) is deprecated at 
/freesurfer/mni/bin/nu_estimate_np_and_em line 165.

Use of ?PATTERN? without explicit operator is deprecated at 
/freesurfer/mni/bin/sharpen_volume line 153.

I think my results should still be OK because it's a warning, but I just 
wanted to make sure.

Thanks,

Eli

Houston Methodist. Leading Medicine.

Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 
specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" 
list 10 years in a row. Designated as a Magnet hospital for excellence in 
nursing. Visit us at houstonmethodist.org. Follow us at 
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Re: [Freesurfer] X graphics issues via SSH

[Rockers, Elijah D.]

After much scouring, this appears to be a problem with XQuartz. I spoke to 
someone on the XQuartz team and they are basically on life-support. It looks 
like support for this may be going down the toilet, and migration to an 
entirely new architecture is needed. I am not the only person experiencing 
problems with GLX either, which apparently qdec and other freesurfer 
applications depends on via SSH.

For now I will look into a work around, VNC/RDP or something of the sort.

Just to keep you up to date, here is the discussion:
https://bugs.freedesktop.org/show_bug.cgi?id=93953#c6

Cheers,

Eli

On 05/11/2016 03:03 PM, Eli wrote:
Hello freesurfers,

Running a Mac Pro, OS X El Capitan 10.11.4
With ATI Radeon Graphics card, and XQuartz v 2.7.9

I am able to run Qdec and freeview perfectly fine on my machine. The problem 
comes when I attempt to SSH into another machine and use these programs (it 
used to work fine, but I am wondering if something in our configuration has 
changed now)

I get the following errors

[belen@picasso:~] freeview
Xlib:  extension "NV-GLX" missing on display "localhost:10.0".
X Error: BadValue (integer parameter out of range for operation) 2
  Extension:150 (Uknown extension)
  Minor opcode: 3 (Unknown request)
  Resource id:  0x0
Abort (core dumped)

[belen@picasso:~] qdec
Xlib:  extension "NV-GLX" missing on display "localhost:10.0".
X Error of failed request:  BadValue (integer parameter out of range for 
operation)
  Major opcode of failed request:  150 (GLX)
  Minor opcode of failed request:  3 (X_GLXCreateContext)
  Value in failed request:  0x0
  Serial number of failed request:  1504
  Current serial number in output stream:  1505

Based on my limited knowledge, It seems likely to be a problem with X / SSH, 
and the graphics card, but I am unsure on how to proceed from here. If anyone 
has any ideas on how to overcome this, I would be incredibly grateful.

The server machine itself also has a monitor, and can run Qdec and Freeview 
fine locally, with no problems. the issue seems to happen over SSH


Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S.News & 
World Report as one of America's "Best Hospitals" in 11 specialties and 
designated as a Magnet hospital for excellence in nursing.  Houston Methodist 
has also been named to FORTUNE®  Magazine's "100 Best Companies to Work For®" 
list for 10 years in a row. Visit us at  houstonmethodist.org. Follow us at  
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[Freesurfer] X graphics issues via SSH

[Rockers, Elijah D.]

Hello freesurfers,

Running a Mac Pro, OS X El Capitan 10.11.4
With ATI Radeon Graphics card, and XQuartz v 2.7.9

I am able to run Qdec and freeview perfectly fine on my machine. The problem 
comes when I attempt to SSH into another machine and use these programs (it 
used to work fine, but I am wondering if something in our configuration has 
changed now)

I get the following errors

[belen@picasso:~] freeview
Xlib:  extension "NV-GLX" missing on display "localhost:10.0".
X Error: BadValue (integer parameter out of range for operation) 2
  Extension:150 (Uknown extension)
  Minor opcode: 3 (Unknown request)
  Resource id:  0x0
Abort (core dumped)

[belen@picasso:~] qdec
Xlib:  extension "NV-GLX" missing on display "localhost:10.0".
X Error of failed request:  BadValue (integer parameter out of range for 
operation)
  Major opcode of failed request:  150 (GLX)
  Minor opcode of failed request:  3 (X_GLXCreateContext)
  Value in failed request:  0x0
  Serial number of failed request:  1504
  Current serial number in output stream:  1505

Based on my limited knowledge, It seems likely to be a problem with X / SSH, 
and the graphics card, but I am unsure on how to proceed from here. If anyone 
has any ideas on how to overcome this, I would be incredibly grateful.

The server machine itself also has a monitor, and can run Qdec and Freeview 
fine locally, with no problems. the issue seems to happen over SSH

Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S.News & 
World Report as one of America's "Best Hospitals" in 11 specialties and 
designated as a Magnet hospital for excellence in nursing.  Houston Methodist 
has also been named to FORTUNE®  Magazine's "100 Best Companies to Work For®" 
list for 10 years in a row. Visit us at  houstonmethodist.org. Follow us at  
twitter.com/MethodistHosp and facebook.com/HoustonMethodist.  
***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist 
and/or its relevant affiliates and may contain restricted and privileged 
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[Freesurfer] XNAT Freesurfer custom datatype

[Rockers, Elijah D.]

Trying to integrate freesurfer data with our XNAT database.

Are there any freesurfer schemas for XNAT available, or is it pretty much I 
have to try to make my own?

Thanks,

--
Elijah Rockers
Research Data Analyst
Houston Methodist Neurological Institute
O: 713 363 7729

Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S.News & 
World Report as one of America's "Best Hospitals" in 11 specialties and 
designated as a Magnet hospital for excellence in nursing.  Houston Methodist 
has also been named to FORTUNE®  Magazine's "100 Best Companies to Work For®" 
list for 10 years in a row. Visit us at  houstonmethodist.org. Follow us at  
twitter.com/MethodistHosp and facebook.com/HoustonMethodist.  
***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist 
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[Freesurfer] HIRING: Research Assistant

[Rockers, Elijah D.]

Hello,

The Houston Methodist Research Institute is hiring for a research 
assistant position. Please see the attached document for details. Please 
also note that candidates must be able to work in the city of Houston 
day-to-day.

If you are interested in applying, please follow the instructions enclosed.

Thank you,

Elijah

Houston Methodist. Leading Medicine.

Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 
specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" 
list 10 years in a row. Designated as a Magnet hospital for excellence in 
nursing. Visit us at houstonmethodist.org. Follow us at 
twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist.

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ResearchAssistantPsychology.docx
Description: ResearchAssistantPsychology.docx
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[Freesurfer] Hiring: Houston, TX - Data Processing/Analysis

[Rockers, Elijah D.]

Hello,

The Nantz National Alzheimer Center, in Houston, TX is looking to fill two 
positions pertaining to neuroimaging and analysis.

Be aware that we cannot accept remote employment, the candidate would have to 
work day-to-day in the city of Houston.

Any interested person is encouraged to review the job postings, which are 
attached.
If you don't see the attachments but you are interested, e-mail me directly and 
I'll make sure you get them.

Thanks,

--
Elijah Rockers
Research Data Analyst
Houston Methodist Neurological Institute
O: 713 363 7729

Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S.News & 
World Report as one of America's "Best Hospitals" in 11 specialties and 
designated as a Magnet hospital for excellence in nursing.  Houston Methodist 
has also been named to FORTUNE®  Magazine's "100 Best Companies to Work For®" 
list for 10 years in a row. Visit us at  houstonmethodist.org. Follow us at  
twitter.com/MethodistHosp and facebook.com/HoustonMethodist.  
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the sender and delete all copies of the message. Thank you.


DataAnalyist.docx
Description: DataAnalyist.docx


PostDoc.docx
Description: PostDoc.docx
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[Freesurfer] voxel value scaling

[Rockers, Elijah D.]

I am interested in finding a way to apply a slope scaling factor to the 
voxel values in a NIfTI image.

I have done this in MATLAB and PMOD so far, but for some reason both 
methods change the origin or otherwise distort the dimensions of the 
image and render it impossible for me to process further.

Something that simply scales the values without touching the header (or 
at least as little as possible) would be great. Is anything like this 
out there?

Thanks,

Eli

Houston Methodist. Leading Medicine.

Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 
specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" 
list 10 years in a row. Designated as a Magnet hospital for excellence in 
nursing. Visit us at houstonmethodist.org. Follow us at 
twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist.

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Re: [Freesurfer] voxel value scaling

[Rockers, Elijah D.]

Great thank you!

On 11/25/2015 11:54 AM, Douglas Greve wrote:
> You can use  fscalc, something like
> fscalc input.nii mul 10 -o output.nii
> I think you can use fslmaths as well
>
> On 11/25/15 12:08 PM, Rockers, Elijah D. wrote:
>> I am interested in finding a way to apply a slope scaling factor to the
>> voxel values in a NIfTI image.
>>
>> I have done this in MATLAB and PMOD so far, but for some reason both
>> methods change the origin or otherwise distort the dimensions of the
>> image and render it impossible for me to process further.
>>
>> Something that simply scales the values without touching the header (or
>> at least as little as possible) would be great. Is anything like this
>> out there?
>>
>> Thanks,
>>
>> Eli
>>
>> Houston Methodist. Leading Medicine.
>>
>> Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 
>> specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" 
>> list 10 years in a row. Designated as a Magnet hospital for excellence in 
>> nursing. Visit us at houstonmethodist.org. Follow us at 
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__twitter.com_MethodistHosp=CwIGaQ=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q=8n4cujoxKHxZUqyKPLhWvF6CDwsoST3qE1-UpVBy2Jc=90ErO06n0uvW3LGGzLcY8_miCTsjq_rUaK5lCHOhs34=
>>   and 
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.facebook.com_HoustonMethodist=CwIGaQ=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q=8n4cujoxKHxZUqyKPLhWvF6CDwsoST3qE1-UpVBy2Jc=2bnJkXlkkepUmpEPsiW94Tl3NWj9KmPs6HSnQ5_Yn0c=
>>  .
>>
>> ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston 
>> Methodist Hospital and/or its relevant affiliates and may contain restricted 
>> and privileged material for the sole use of the intended recipient(s). Any 
>> review, use, distribution or disclosure by others is strictly prohibited. If 
>> you are not the intended recipient (or authorized to receive for the 
>> recipient), please contact the sender and delete all copies of the message. 
>> Thank you.
>>
>> ___
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>>
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[Freesurfer] Extract single time frame

[Rockers, Elijah D.]

Hello again,

I have a large time series in dicom or .nii format. I am interested in 
extracting a single time frame from it. I did this before, I believe 
with freesurfer, but I have somehow forgot the name of the command, and 
I can't seem to find it. I believe it could be used to specify 
particular regions of the volume, as well as time. I need the entire 
volume, still, but only one frame.

Thanks in advance!

Eli

Houston Methodist. Leading Medicine.

Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 
specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" 
list 10 years in a row. Designated as a Magnet hospital for excellence in 
nursing. Visit us at houstonmethodist.org. Follow us at 
twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist.

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Re: [Freesurfer] Extract single time frame

[Rockers, Elijah D.]

Thank you, I was not aware of the #frame extension!

Eli

On 10/26/2015 10:26 AM, Bruce Fischl wrote:
Hi Eli

a couple of different ways would work. The frams are numbered starting at 0 for 
the first one. So for frame #5 (the 6th one) it would be:

mri_convert -nth 5 file.nii file.frame5.nii

Alternatively, all of our tools accept the extension # so you could do:

mri_convert file.nii#5 file.frame5.nii

cheers
Bruce


On Mon, 26 Oct 2015, Rockers, Elijah D. wrote:

Hello again,

I have a large time series in dicom or .nii format. I am interested in
extracting a single time frame from it. I did this before, I believe
with freesurfer, but I have somehow forgot the name of the command, and
I can't seem to find it. I believe it could be used to specify
particular regions of the volume, as well as time. I need the entire
volume, still, but only one frame.

Thanks in advance!

Eli

Houston Methodist. Leading Medicine.

Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 
specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" 
list 10 years in a row. Designated as a Magnet hospital for excellence in 
nursing. Visit us at houstonmethodist.org. Follow us at 
https://urldefense.proofpoint.com/v2/url?u=http-3A__twitter.com_MethodistHosp=CwIDaQ=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q=PeUntES685F-UfQu3Mz3RO0sFtsKb-3nDeXpO2JuUcY=3UpBlEjEeJhVd290VHDldyQHfSHUQeToQFczPifNSzU=
  and 
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.facebook.com_HoustonMethodist=CwIDaQ=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q=PeUntES685F-UfQu3Mz3RO0sFtsKb-3nDeXpO2JuUcY=VkMpRavoHekJ3Xu6J1Rm8UEbgbWu5NEOyRz85C9olgk=
 .

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Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S.News & 
World Report as one of America's "Best Hospitals" in 11 specialties and 
designated as a Magnet hospital for excellence in nursing.  Houston Methodist 
has also been named to FORTUNE®  Magazine's "100 Best Companies to Work For®" 
list for 10 years in a row. Visit us at  houstonmethodist.org. Follow us at  
twitter.com/MethodistHosp and facebook.com/HoustonMethodist.  
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[Freesurfer] Exporting ROIs as .nii

[Rockers, Elijah D.]

Hello,

We are interested in finding a way to use particular parcellations from 
Freesurfer in a separate program. For instance, we are very happy with 
the way Freesurfer parcellates the Choroid Plexus and separates the 
Cerebellum into white and gray matter regions, and would like to import 
these regions into another program for analysis. This other program 
(PMOD) can import .nii files as templates. We have been so far 
unsuccessful at importing the regions, but believe it should be possible.

Is there some way to achieve this?

Thanks,

Eli

Houston Methodist. Leading Medicine.

Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 
specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" 
list 10 years in a row. Designated as a Magnet hospital for excellence in 
nursing. Visit us at houstonmethodist.org. Follow us at 
twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist.

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