Re: [Freesurfer] about FreeSurfer QA tools errors

[Xin Qi]

External Email - Use Caution

Thanks, Andrew for replying.

Best regards
Xin

On Thu, Aug 12, 2021 at 10:52 AM Hoopes, Andrew 
wrote:

> Hi Xin,
>
>
>
> Are you using the QA tools from
> https://secure-web.cisco.com/1M0BdrfUAFtsM7sCclEujxPoDhQ5T-YCM-ykHvPvQIzmG_tDuRSClxmvQRHcOLru6z4xrXIjTZIT104Ct8uSM3gscxbonfi7XGqF3eBz7SPBuDNDU5RxPWHo2xEfonfrIBEAub-mkPwEufzehwSGtfJ1j2WQ9suUggMzJMav1fpuEXGW7uTQ__T_oNSyjwPlURPYCVZRlrR6-j_Fi1pas_8Hj7Mf_zYvzQ9s5Z1hNPhUAFNuTocmDgaVIdNPQXhHLWHZuRF_db3Q-cOZ4x8MRwA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FQATools?
>  Those are specific to
> FS 5.3 (we should update the wiki). v7.1 includes an executable named
> `qatools.py` that functions similarly.
>
>
>
> best
>
> Andrew
>
>
>
> *From: *freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Xin Qi <
> xinqi2...@gmail.com>
> *Date: *Thursday, August 12, 2021 at 12:00 AM
> *To: *Freesurfer support list 
> *Subject: *[Freesurfer] about FreeSurfer QA tools errors
>
> *External Email - Use Caution        *
>
> Hi Freesurfer Community Support Team:
>
>
>
> We would like to use FreeSurfer QA tools.
>
>
>
> After installing it, I tested it on one subject that finished Freesurfer
> recon-all processing using the latest FreeSurfer 7.1. but got errors that
> seem many files are missing in the mri, surf, stat folders created by
> FreeSurfer.
>
>
>
> I attach the recon_checker summary log and zipped snaps file for your
> reference.
>
>
>
> Looking forward to hearing from you. Thank you very much.
>
>
>
> Best regards
>
> Xin
> ___
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Re: [Freesurfer] about FreeSurfer QA tools errors

[Hoopes, Andrew]

Hi Xin,

Are you using the QA tools from 
https://surfer.nmr.mgh.harvard.edu/fswiki/QATools? Those are specific to FS 5.3 
(we should update the wiki). v7.1 includes an executable named `qatools.py` 
that functions similarly.

best
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Xin Qi 

Date: Thursday, August 12, 2021 at 12:00 AM
To: Freesurfer support list 
Subject: [Freesurfer] about FreeSurfer QA tools errors

External Email - Use Caution
Hi Freesurfer Community Support Team:

We would like to use FreeSurfer QA tools.

After installing it, I tested it on one subject that finished Freesurfer 
recon-all processing using the latest FreeSurfer 7.1. but got errors that seem 
many files are missing in the mri, surf, stat folders created by FreeSurfer.

I attach the recon_checker summary log and zipped snaps file for your reference.

Looking forward to hearing from you. Thank you very much.

Best regards
Xin
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addressed. If you believe this e-mail was sent to you in error and the e-mail 
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Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If 
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[Freesurfer] QA tools

[Micah Rhodes]

Dear Freesurfer list,

As I have used the QA tools on a couple recon-all jobs, I have run into an
error when running recon_checker QA tools. The QA tools are not able to
read many of the output files from recon-all, in the "label" directory. As
I look back into the label directory, this is because many of my files
after running recon have an "_exvivo" stem. For example, the QA tools
cannot read the "../label/lh.BA1.label" file because in my subject
directory, as it is named "../label/lh.BA1_exvivo.label". And the same is
true for many other files.

After searching online for solutions to this problem I have not found any
way to eliminate the _exvivio stem, but I understand that exvivo data has
been used to increase the quality of images for FS v6. Is there a way to
fix this when running recon-all? Or, is this problem occurring because I'm
using QAtools1.2 with FS v6.0?

Best,
Micah
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Re: [Freesurfer] QA tools for FS vs 6.0

[Antonietta Pepe]

Dear Falk,

Thanks for your replay. 
I tried getting in contact with him more than a month ago without success, this 
is why I was hoping in a more official release. 
I did use a different email address though, probably not the good one?

Best,
Antonietta


> On 23 Aug 2017, at 17:32, Falk Lüsebrink <falk.luesebr...@ovgu.de> wrote:
> 
> Dear Antonietta,
>  
> I don’t know of any official statement in that regard, however, Yong Li 
> (CC’ed) seems to have updated the QA tools working with FS 6 in April. He may 
> share his code.
>  
> Best,
> Falk
>  
> Von: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Antonietta Pepe
> Gesendet: Mittwoch, 23. August 2017 16:47
> An: freesurfer@nmr.mgh.harvard.edu
> Betreff: [Freesurfer] QA tools for FS vs 6.0
>  
> Dear FreeSurfer list,
> is any of you aware of a new version of the QA (quality assessment) tools 
> <https://surfer.nmr.mgh.harvard.edu/fswiki/QATools 
> <https://surfer.nmr.mgh.harvard.edu/fswiki/QATools>> working for FS vs 6.0? 
> Should I expect a new release in the near feature?
>  
> Kind regards,
>  
> Antonietta
>  
> ANTONIETTA PEPE
> IMN, Institut des Maladies Neurodégénératives, UMR 5293
> Equipe 5 : GIN, Groupe d’Imagerie Neurofonctionnelle, CEA - CNRS - Université 
> de Bordeaux
> Université de Bordeaux
> 146 rue Léo Saignat - CS 61292 - Case 28
> 33 076 Bordeaux cedex
> http://www.imn-bordeaux.org/ <http://www.imn-bordeaux.org/>
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Re: [Freesurfer] QA tools for FS vs 6.0

[Falk Lüsebrink]

Dear Antonietta,

I don’t know of any official statement in that regard, however, Yong Li (CC’ed) 
seems to have updated the QA tools working with FS 6 in April. He may share his 
code.

Best,
Falk

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Antonietta Pepe
Gesendet: Mittwoch, 23. August 2017 16:47
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] QA tools for FS vs 6.0

Dear FreeSurfer list,

is any of you aware of a new version of the QA (quality assessment) tools 
<https://surfer.nmr.mgh.harvard.edu/fswiki/QATools> working for FS vs 6.0? 
Should I expect a new release in the near feature?



Kind regards,



Antonietta

ANTONIETTA PEPE
IMN, Institut des Maladies Neurodégénératives, UMR 5293
Equipe 5 : GIN, Groupe d’Imagerie Neurofonctionnelle, CEA - CNRS - Université 
de Bordeaux
Université de Bordeaux
146 rue Léo Saignat - CS 61292 - Case 28
33 076 Bordeaux cedex
http://www.imn-bordeaux.org/


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[Freesurfer] QA tools for FS vs 6.0

[Antonietta Pepe]

Dear FreeSurfer list, 
is any of you aware of a new version of the QA (quality assessment) tools < [ 
https://surfer.nmr.mgh.harvard.edu/fswiki/QATools | 
https://surfer.nmr.mgh.harvard.edu/fswiki/QATools ] > working for FS vs 6.0? 
Should I expect a new release in the near feature?

Kind regards,

Antonietta 

ANTONIETTA PEPE 
IMN, Institut des Maladies Neurodégénératives, UMR 5293 
Equipe 5 : GIN, Groupe d’Imagerie Neurofonctionnelle, CEA - CNRS - Université 
de Bordeaux 
Université de Bordeaux 
146 rue Léo Saignat - CS 61292 - Case 28 
33 076 Bordeaux cedex 
[ http://www.imn-bordeaux.org/ | http://www.imn-bordeaux.org/ ] 



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Re: [Freesurfer] QA Tools v1.2 and future release

[Yong Li]

Dear Freesurfer Experts,

Please excuse my long email yesterday.

Now, I finished code update of the outlier detection part for brainstem
substructures (bs) and Hippocampal Subfields (hc) modules. Code updated in
the similar way as my last email except that I combined the output of both
modules to simplify the process. The following log files might show some
clue of my exploration:

YongbshcLUT (like asegLUT_112511):

Medulla 0.287988 +/- 0.0304379
Pons 0.864817 +/- 0.128019
SCP 0.0161611 +/- 0.0030778
Midbrain 0.388938 +/- 0.038842
Whole_brainstem 1.8246 +/- 0.184472
Left-Hippocampal_tail 0.0291617 +/- 0.00437039
Left-subiculum 0.0237801 +/- 0.0044348
Left-CA1 0.0387709 +/- 0.00612168
Left-hippocampal-fissure 0.00944849 +/- 0.00188347
Left-presubiculum 0.0177329 +/- 0.00272706
Left-parasubiculum 0.00372024 +/- 0.000876862
Left-molecular_layer_HP 0.0320802 +/- 0.00806223
Left-GC-ML-DG 0.0186971 +/- 0.00308382
Left-CA3 0.0120106 +/- 0.00198279
Left-CA4 0.0132618 +/- 0.00261687
Left-fimbria 0.00371701 +/- 0.00166146
Left-HATA 0.0031189 +/- 0.000692806
Left-Whole_hippocampus 0.190022 +/- 0.0246413
Right-Hippocampal_tail 0.030817 +/- 0.00496078
Right-subiculum 0.0248689 +/- 0.00427691
Right-CA1 0.0370719 +/- 0.00873442
Right-hippocampal-fissure 0.0103329 +/- 0.00187117
Right-presubiculum 0.0178487 +/- 0.00260947
Right-parasubiculum 0.00380418 +/- 0.000861778
Right-molecular_layer_HP 0.032938 +/- 0.00448073
Right-GC-ML-DG 0.0168729 +/- 0.00304788
Right-CA3 0.0130893 +/- 0.00239818
Right-CA4 0.0143492 +/- 0.00281808
Right-fimbria 0.00438099 +/- 0.00176098
Right-HATA 0.00338842 +/- 0.0006037
Right-Whole_hippocampus 0.198797 +/- 0.0243668

an example subject's bshc.stats (like aseg.stats):

Medulla 4288.386728
Pons 12836.783824
SCP 194.446727
Midbrain 8306.988464
Whole_brainstem 22293.878740
Left-Hippocampal_tail 462.086606
Left-subiculum 307.970217
Left-CA1 816.878818
Left-hippocampal-fissure 118.986208
Left-presubiculum 227.392060
Left-parasubiculum 84.381831
Left-molecular_layer_HP 841.496111
Left-GC-ML-DG 238.308049
Left-CA3 183.383724
Left-CA4 196.098618
Left-fimbria 73.990998
Left-HATA 36.237082
Left-Whole_hippocampus 2838.187477
Right-Hippocampal_tail 408.832729
Right-subiculum 388.667888
Right-CA1 801.601831
Right-hippocampal-fissure 132.071091
Right-presubiculum 242.179137
Right-parasubiculum 43.414171
Right-molecular_layer_HP 487.298072
Right-GC-ML-DG 246.283617
Right-CA3 164.849646
Right-CA4 209.108368
Right-fimbria 90.291400
Right-HATA 42.073898
Right-Whole_hippocampus 2791.300419

icv.txt (actually eITV instead of ICV):

1420463.178113

bshc_outliers.log:

Subject 008  Right-HATA value .002080900 is an outlier ...

Note: all data here are kind of simulation results because of data safety
reason and these logs only serve as signs of correct code update.

I guess that both the only output of bs and hc (bshc.stats) is segment
volume, not the 'normMean normStdDev ...' in aseg.stats.
So is it senseful to include those 'norm*' measures in the bs & hc modules
in the future?
BTW, is there an advantage to use normMax / eITV rather than normMean /
eITV in outlier detection in theory?

Thank you very much again!

I wish all of you a nice weekend!

Best regards,

Yong
_
Yong Li,  PhD
Department of Neurology,
Klinikum rechts der Isar,
Technische Universität München,
Munich, Germany

On Thu, Apr 6, 2017 at 11:36 AM, Yong Li  wrote:

> Dear Freesurfer Experts,
>
> As one of the new freesurfers, I really appreciate the excellent work of
> authors as well as great support of users' forum.
>
> A good guess of mine is that authors, e.g., Vasanth or Louis etc., are
> busy updating QA tools after the FSv6 release since the QA Tools v1.2 was
> written for FSv5.3. If so, is it possible to provide an estimated release
> date please so as to adjust my plan? Thanks for understanding!
>
> In case, it might take a while to release the next QA Tool, may I dare to
> provide my attempts of code updating of some functions in QA Tools? The
> following are the brief list of code adapting steps:
> 1. modified codes for generating file order list in recon_checker;
> 2. modified codes for matching segment names for instance from
> DefaultAsegMeans.txt in gparcmean_from_table;
> 3. adapted default_FOF and default_status_log for FSv6.
>
> After these adaptation, QA Tools ran through and I only encountered some
> 'syntax error' in terminal for 2 segments, 5th-Ventricle and
> WM-hypointensities, that I have to ask the experts to guide me through this
> point if it's of your interests. To ensure the QA Tools functioning well, I
> tested 116 elderly patients and detected reasonable outliers per patient.
> Therefore, I would like to double that my code updating based on my general
> understanding of QA Tool still fit to the basic purpose of authors by
> asking the following theoretical questions:
>
> 1. SNR and segments outliers detection are measures of quality assessment
> in QA Tools. Have other 

[Freesurfer] QA Tools v1.2 and future release

[Yong Li]

Dear Freesurfer Experts,

As one of the new freesurfers, I really appreciate the excellent work of
authors as well as great support of users' forum.

A good guess of mine is that authors, e.g., Vasanth or Louis etc., are busy
updating QA tools after the FSv6 release since the QA Tools v1.2 was
written for FSv5.3. If so, is it possible to provide an estimated release
date please so as to adjust my plan? Thanks for understanding!

In case, it might take a while to release the next QA Tool, may I dare to
provide my attempts of code updating of some functions in QA Tools? The
following are the brief list of code adapting steps:
1. modified codes for generating file order list in recon_checker;
2. modified codes for matching segment names for instance from
DefaultAsegMeans.txt in gparcmean_from_table;
3. adapted default_FOF and default_status_log for FSv6.

After these adaptation, QA Tools ran through and I only encountered some
'syntax error' in terminal for 2 segments, 5th-Ventricle and
WM-hypointensities, that I have to ask the experts to guide me through this
point if it's of your interests. To ensure the QA Tools functioning well, I
tested 116 elderly patients and detected reasonable outliers per patient.
Therefore, I would like to double that my code updating based on my general
understanding of QA Tool still fit to the basic purpose of authors by
asking the following theoretical questions:

1. SNR and segments outliers detection are measures of quality assessment
in QA Tools. Have other factors such as subject's motion, image bias,
resolution etc. been considered in QA Tools or future release? The default
SNR threshold is 16 based on any reference? The max SNR of my patients so
far is 32. Any idea of scores of healthy elderly controls?

2. The QA Tools v1.2 analyzes aseg.stats output. Is it possible to include
output of brainstem substructures and HippocampalSubfields of FSv6? If yes,
I would like to adapt the codes and provide you some feedback if you think
that I can help bit.

3. Future directions mentioned in QA Tools wiki site are interesting and
thoughtful. Are other features like 'Detect outliers in aparc and aparc2009
volumes' on the way?

4. Is there a function to summarize all QA measures to csv files, like the
quantifyBrainstemStructures.sh in brainstem substructures?

Thank you in advance!

Kind regards,

Yong Li, PhD
_
Department of Neurology,
Klinikum rechts der Isar,
Technische Universität München,
Munich, Germany
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Re: [Freesurfer] QA tools

[Lee Tirrell]

Hi John,

Do tkmedit and tksurfer work by themselves? You can try this by running the 
following commands (assuming your SUBJECTS_DIR is set to the location 
containinng your subject ALS-0038):


tkmedit ALS-0038 norm.mgz
tksurfer ALS-0038 rh pial

Best,
Lee


On Tue, 13 Sep 2016, John Anderson wrote:



Hello, FS experts,
I am trying to use QA tool: 
I ran the following command 
recon_checker -snaps-only -s-file subjects.txt
 
The script output the following:
X11 connection rejected because of wrong authentication.
GLUT: Fatal Error in tkmedit.bin: could not open display: localhost:12.0
X11 connection rejected because of wrong authentication.
GLUT: Fatal Error in tksurfer.bin: could not open display: localhost:12.0
X11 connection rejected because of wrong authentication.
GLUT: Fatal Error in tksurfer.bin: could not open display: localhost:12.0
     Taking snapshots for subject ALS-0038
X11 connection rejected because of wrong authentication.
GLUT: Fatal Error in tkmedit.bin: could not open display: localhost:12.0
X11 connection rejected because of wrong authentication.
GLUT: Fatal Error in tksurfer.bin: could not open display: localhost:12.0
X11 connection rejected because of wrong authentication.
GLUT: Fatal Error in tksurfer.bin: could not open display: localhost:12.0
 
 
At the end it said that he process finshed. I checked the AQ folder and the 
snaps where not there 
 
Any suggestions!
 
Bests,
John 

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[Freesurfer] QA tools

[John Anderson]

Hello, FS experts,

I am trying to use QA tool: 

I ran the following command 

recon_checker -snaps-only -s-file subjects.txt

 

The script output the following:


X11 connection rejected because of wrong authentication.
GLUT: Fatal Error in tkmedit.bin: could not open display: localhost:12.0
X11 connection rejected because of wrong authentication.
GLUT: Fatal Error in tksurfer.bin: could not open display: localhost:12.0
X11 connection rejected because of wrong authentication.
GLUT: Fatal Error in tksurfer.bin: could not open display: localhost:12.0

     Taking snapshots for subject ALS-0038
X11 connection rejected because of wrong authentication.
GLUT: Fatal Error in tkmedit.bin: could not open display: localhost:12.0
X11 connection rejected because of wrong authentication.
GLUT: Fatal Error in tksurfer.bin: could not open display: localhost:12.0
X11 connection rejected because of wrong authentication.
GLUT: Fatal Error in tksurfer.bin: could not open display: localhost:12.0

 

 

At the end it said that he process finshed. I checked the AQ folder and the snaps where not there 

 

Any suggestions!


 

Bests,
John 
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[Freesurfer] QA Tools : All in errors for aseg outliers detection

[Matthieu Vanhoutte]

Dear FS experts,

I tried to run the QA Tools on a subject with the following command:
*${QA_TOOLS}/recon_checker -s 207043_M0_2010-10-07 -outputFOF
${SUBJECTS_DIR}/FOF -gen-outputFOF -gen-asegLUT
${SUBJECTS_DIR}/AsegOutliers*

But I got all errors concerning the detection of Aseg outliers:
*Making aseg look-up table, /NAS/tupac/matthieu/FS5.3//AsegOutliers*
*parsing arguments ...*
*checking parameters ...*
*MeanFile is /NAS/tupac/matthieu/FS5.3//AsegOutliers*
*checking logs ...*
*done checking logs ...*
*done checking parameters ...*
*moving previous log files to *.bak*
*done moving previous log files*
*Processing each subcortical label ...*
*(standard_in) 1: syntax error*
*gawk: /home/matthieu/programs/QAtools_v1.1/gstd.awk:22: (FILENAME=- FNR=1)
fatal: division by zero attempted*
*(standard_in) 1: syntax error*
*(standard_in) 1: syntax error*
*(standard_in) 1: syntax error*
*(standard_in) 1: syntax error*
*(standard_in) 1: syntax error*
*(standard_in) 1: syntax error*




*-Checking asegs for outliers...Using asegLUT:
/NAS/tupac/matthieu/FS5.3//AsegOutliersparsing arguments ...checking
parameters ...checking logs ...done checking logs ...done checking
parameters ...moving previous log files to *.bakdone moving previous log
filesProcessing each subcortical label ...(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error(standard_in) 1: syntax
error(standard_in) 1: syntax error*
Please find attached the recon_checker summary.

Thanks in advance for any help !

Best regards,
Matthieu

Tue Jun 14 11:07:11 CEST 2016


SUBJECTS_DIR: /NAS/tupac/matthieu/FS5.3/ 

Generating file order list using subject 207043_M0_2010-10-07
 Using file list: /NAS/tupac/matthieu/FS5.3//QA/local_default_output_order_file


checking subcortical label: Left-Cerebral-Exterior, 0 +/-
checking subcortical label: Left-Cerebral-White-Matter, 0 +/-
checking subcortical label: Left-Cerebral-Cortex, 0 +/-
checking subcortical label: Left-Lateral-Ventricle, 0 +/-
checking subcortical label: Left-Inf-Lat-Vent, 0 +/-
checking subcortical label: Left-Cerebellum-Exterior, 0 +/-
checking subcortical label: Left-Cerebellum-White-Matter, 0 +/-
checking subcortical label: Left-Cerebellum-Cortex, 0 +/-
checking subcortical label: Left-Thalamus, 0 +/-
checking subcortical label: Left-Thalamus-Proper, 0 +/-
checking subcortical label: Left-Caudate, 0 +/-
checking subcortical label: Left-Putamen, 0 +/-
checking subcortical label: Left-Pallidum, 0 +/-
checking subcortical label: 3rd-Ventricle, 0 +/-
checking subcortical label: 4th-Ventricle, 0 +/-
checking subcortical label: Brain-Stem, 0 +/-
checking subcortical label: Left-Hippocampus, 0 +/-
checking subcortical label: Left-Amygdala, 0 +/-
checking subcortical label: Left-Insula, 0 +/-
checking subcortical label: Left-Operculum, 0 +/-
checking subcortical label: Line-1, 0 +/-
checking subcortical label: Line-2, 

[Freesurfer] QA Tools, inespecific error: parse error (standard_in)

[Julio Alberto González Torre]

Hi Freesurfer users,

I am recently testing the QA Tools in order to identify errors, especially
aseg outliers.

I don''t know if this is the right place to make this question, but I
followed the instructions for download, install and usage, explained on:
https://surfer.nmr.mgh.harvard.edu/fswiki/QATools

I installed QATools and its dependencies: ImageMagick and gwak

When I run the QA Tools there is an unespected error when trying to get
aseg values:

Checking asegs for outliers...
> Using asegLUT: aseg_output.txt
> parsing arguments ...
> checking parameters ...
> checking logs ...
> done checking logs ...
> done checking parameters ...
> moving previous log files to *.bak
> done moving previous log files
> Processing each subcortical label ...
> (standard_in) 1: parse error
> (standard_in) 1: parse error
> (standard_in) 1: parse error
> (standard_in) 1: parse error
> (standard_in) 1: parse error
> (standard_in) 1: parse error
> (standard_in) 1: parse error
> (standard_in) 1: parse error
> (standard_in) 1: parse error
> (standard_in) 1: parse error
>

...
(several times)


I can't identify why this error happens, but the output text about aseg
values file is empty. The snaps output is correct.

Does anybody know why is this happening? Or is there any alternative to
check outliers?

Thanks.
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Re: [Freesurfer] QA tools

[angela . favaro]

Thank you Bruce and MIke!
I was not really looking for something INSTEAD of manual inspection, but
for a measure of the quality of my dataset similarly to what is
reccomended for functional MRI (in that case a SNR below 100 can be
considered a criterion of exclusion).
What are the meaning of these metrics?

Thank you
Angela


> Hi Mike
>
> I agree! It's really hard to detect e.g. the tip of the nose wrapping
> into occipital cortex. I was thinking more of the tools that generate
> pages of snapshots so you can quickly scan through datasets to find
> dramatic failures
>
> cheers
> Bruce
> On Mon, 23 Nov 2015, Harms, Michael wrote:
>
>>
>> In my experience, none of the quantitative "SNR/CNR" metrics available
>> through various FS tools (some of which may be part of the QATools)
>> replace the need to manually  inspect the results.  Some truly awful
>> data
>> may show up as "outliers", but you can't count on those values to flag
>> all
>> the data with problems.
>>
>> cheers,
>> -MH
>>
>> --
>> Michael Harms, Ph.D.
>>
>> ---
>> Conte Center for the Neuroscience of Mental Disorders
>> Washington University School of Medicine
>> Department of Psychiatry, Box 8134
>> 660 South Euclid Ave.Tel: 314-747-6173
>> St. Louis, MO  63110Email: mha...@wustl.edu
>>
>>
>>
>>
>> On 11/23/15 11:16 AM, "angela.fav...@unipd.it" 
>> wrote:
>>
>> Hi all,
>>
>> I am starting to use QAtools in Freesurfer.
>> The scripts are working well, but I have two problems:
>>
>> 1. the interpretation of output is the first. Are there ranges of
>> normality for SNR and intensity? Could you please give me some reference
>> or link about how to interpret these data? Or do I only need to look at
>> outliers (or something similar)? My values are in the range between 19
>> and
>> 25 (and the subject with 19 have problems at visual inspection).
>> The script also outputs 'no outlier' in all my subjects. Which type of
>> outliers is it referring to?
>>
>> 2. I have also problems in getting snapshots, but I think this is due to
>> my
>> poor experience with setting paths of ImageMagick. I am using a MAC OSX
>> 10.6.8 and I used (tcsh)
>> setenv MAGICK_HOME /Applications/ImageMagick-6.9.2/bin
>> but probably this is not enough (any suggestion is greatly apreciated).
>>
>> Thank you for any help you can give me
>>
>> Best wishes
>>
>> Angela
>>
>>
>>
>>
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>>
>>
>> The information in this e-mail is intended only for the person to whom
>> it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in
>> error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>>
>> 
>> The materials in this message are private and may contain Protected
>> Healthcare Information or other information of a sensitive nature. If
>> you are not the intended recipient, be advised that any unauthorized
>> use, disclosure, copying or the taking of any action in reliance on the
>> contents of this information is strictly prohibited. If you have
>> received this email in error, please immediately notify the sender via
>> telephone or return mail.
>>
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>>
>>
>>
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Re: [Freesurfer] QA tools

[Bruce Fischl]

Hi Mike

I agree! It's really hard to detect e.g. the tip of the nose wrapping 
into occipital cortex. I was thinking more of the tools that generate 
pages of snapshots so you can quickly scan through datasets to find 
dramatic failures

cheers
Bruce
On Mon, 23 Nov 2015, Harms, Michael wrote:

>
> In my experience, none of the quantitative "SNR/CNR" metrics available
> through various FS tools (some of which may be part of the QATools)
> replace the need to manually  inspect the results.  Some truly awful data
> may show up as "outliers", but you can't count on those values to flag all
> the data with problems.
>
> cheers,
> -MH
>
> --
> Michael Harms, Ph.D.
>
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave.Tel: 314-747-6173
> St. Louis, MO  63110Email: mha...@wustl.edu
>
>
>
>
> On 11/23/15 11:16 AM, "angela.fav...@unipd.it" 
> wrote:
>
> Hi all,
>
> I am starting to use QAtools in Freesurfer.
> The scripts are working well, but I have two problems:
>
> 1. the interpretation of output is the first. Are there ranges of
> normality for SNR and intensity? Could you please give me some reference
> or link about how to interpret these data? Or do I only need to look at
> outliers (or something similar)? My values are in the range between 19 and
> 25 (and the subject with 19 have problems at visual inspection).
> The script also outputs 'no outlier' in all my subjects. Which type of
> outliers is it referring to?
>
> 2. I have also problems in getting snapshots, but I think this is due to my
> poor experience with setting paths of ImageMagick. I am using a MAC OSX
> 10.6.8 and I used (tcsh)
> setenv MAGICK_HOME /Applications/ImageMagick-6.9.2/bin
> but probably this is not enough (any suggestion is greatly apreciated).
>
> Thank you for any help you can give me
>
> Best wishes
>
> Angela
>
>
>
>
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
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> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
>
> 
> The materials in this message are private and may contain Protected 
> Healthcare Information or other information of a sensitive nature. If you are 
> not the intended recipient, be advised that any unauthorized use, disclosure, 
> copying or the taking of any action in reliance on the contents of this 
> information is strictly prohibited. If you have received this email in error, 
> please immediately notify the sender via telephone or return mail.
>
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>
>
>
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[Freesurfer] QA tools

[angela . favaro]

Hi all,

I am starting to use QAtools in Freesurfer.
The scripts are working well, but I have two problems:

1. the interpretation of output is the first. Are there ranges of
normality for SNR and intensity? Could you please give me some reference
or link about how to interpret these data? Or do I only need to look at
outliers (or something similar)? My values are in the range between 19 and
25 (and the subject with 19 have problems at visual inspection).
The script also outputs 'no outlier' in all my subjects. Which type of
outliers is it referring to?

2. I have also problems in getting snapshots, but I think this is due to my
poor experience with setting paths of ImageMagick. I am using a MAC OSX
10.6.8 and I used (tcsh)
setenv MAGICK_HOME /Applications/ImageMagick-6.9.2/bin
but probably this is not enough (any suggestion is greatly apreciated).

Thank you for any help you can give me

Best wishes

Angela




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[Freesurfer] QA-Tools installation problem

[Baur Volker]

Dear experts,
we have a problem with installation of QA-Tools. It seems that it is not 
because of ImageMagick and Gawk not being properly installed, but rather there 
seems to be some problems with environmental variables. For example, when 
changing into QA-Tools directory in the terminal and starting recon_checker, we 
get command not found. When recon_checker is prompted with full path 
information, the parameters are listed in the help condition. So it seems 
that the application could be found. However, as soon as parameter -s and a 
subject variable is entered to start the quality assessment of one subject, we 
get: QA_TOOLS: undefined variable.
Could you specify which information should be included in the .profile file? 
We are currently working with bash shell.

Thanks very much for any hints and comments,
Volker

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[Freesurfer] QA tools outliers, use of -gen-asegLUT

[charles laidi]

Dear freesurfers,

After reading the documentation on freesurfer web site and searching in the
mail archive I wasn't able to find an answer to my question.
I'm trying to perform cerebellar segmentation on 100 subjects.
The recon-all step went well : every t1 image finished without error when
I checked the recon-all log.
I checked the segmentation result with tmedit and tksurfer (following the
recommendation of freesurfer website). I wasn't able to find any problem.
After that I use the QA tool. Again, after looking at the snapshots the
result appeared correct to me. But for each t1 image, there were between 36
and 45 outliers. So I used the -gen-asegLUT option as suggested in the mail
archive (Please find the result below for a t1 image called as100351_conv),
but wasn't able to understand the result.
The questions I would like to ask you are :

1)What should I do to correct the outliers ?

2) I don't understand this message :
ERROR: Actual file order disagrees with common file order for subject
as100351_conv
and this command doesn't work recon-all -make all -subjid as100351_conv

3) I don't understand this message :
checking subcortical label: Left-Cerebellum-White-Matter, . +/- .
as100351_conv Left-Cerebellum-White-Matter value 1.209679200 is an
outlier (avg = . +/- .)...
The value that appears to be an outliers doesn't match with the value that
I found in Asegstats for Left-Cerebellum-White-Matter.

Thanks a lot for your help, have a nice weekend.

Charles Laidi. (medcharleslaidi (a t) gmail.com)

-
Running recon_checker on:
mercredi 16 janvier 2013, 22:47:04 (UTC+0100)
-
Most recent FreeSurfer version used to process this subject:
/i2bm/local/freesurfer/bin/recon-all
-
All FreeSurfer versions used to process this subject:
/i2bm/local/freesurfer/bin/recon-all
-
Checking all output files exist...
 Running command:
/home/charles/Bureau/QAtools_v1.1/recon_all_output_file_checker -subjid
as100351_conv -slog
/home/charles/Bureau/group_complique//as100351_conv/scripts/recon_checker.log
-sumlog
/home/charles/Bureau/group_complique//QA/recon_checker.ALL.summary.log
-outputfileorderfile /home/charles/Bureau/QAtools_v1.1/default_FOF_FSv5.1
 mri/rawavg.mgz last modified 2012-12-14 05:50:00.0 +0100
 mri/orig.mgz last modified 2012-12-14 05:50:06.0 +0100

 ERROR: Actual file order disagrees with common file order for subject
as100351_conv

 At least one step in the recon-all stream has been skipped or
 rerun out of order.  Run the following command to rerun any steps
 which were skipped or for which the output has been modified.

  recon-all -make all -subjid as100351_conv

 Alternatively, examine the ReconAllTable for your version of FreeSurfer
 to identify the recon-all step where the discrepancy is occuring and
rerun
 every recon-all step from that point forward.  This subject may have
been
 processed with a different version of FreeSurfer other than the version
 used to create the common file order file (based on v5.1 by default if
not
 specified by the user).  Consider generating an output file order file
for
 your specific dataset using the 'genoutputorderfile' flag.
 See the '-help' flag for details.

 actual order    common order:
 ..    .
 mri/rawavg.mgz    mri/rawavg.mgz
 mri/orig.mgz    mri/orig.mgz
 mri/transforms/talairach.xfm    mri/transforms/talairach.auto.xfm
 mri/transforms/talairach.auto.xfm    mri/transforms/talairach.xfm
 mri/nu.mgz    mri/nu.mgz
 mri/T1.mgz    mri/T1.mgz
 mri/brainmask.mgz    mri/brainmask.auto.mgz
 ..    .
-
Checking status log output...
Running command:
/home/charles/Bureau/QAtools_v1.1/recon_all_status_log_checker -subjid
as100351_conv -details -slog
/home/charles/Bureau/group_complique//as100351_conv/scripts/recon_checker.log
-sumlog
/home/charles/Bureau/group_complique//QA/recon_checker.ALL.summary.log
Using status log:
/home/charles/Bureau/QAtools_v1.1/default_status_log_FSv5.1.log

as100351_conv COMPLETE
-
Checking asegs for outliers...
Using asegLUT: test4
Running command:
/home/charles/Bureau/QAtools_v1.1/recon_all_aseg_outlier_checker -subjid
as100351_conv -LookupMeansFromFile test4 -slog
/home/charles/Bureau/group_complique//as100351_conv/scripts/recon_checker.log
-sumlog
/home/charles/Bureau/group_complique//QA/recon_checker.ALL.summary.log
checking subcortical label: Left-Cerebral-Exterior, 0 +/-
checking subcortical label: Left-Cerebral-White-Matter, . +/- .
checking subcortical label: Left-Cerebral-Cortex, . +/- .
checking subcortical label: Left-Lateral-Ventricle, . +/- .
as100351_conv Left-Lateral-Ventricle value .541890500 is an outlier
(avg = . +/- .)...
checking subcortical label: Left-Inf-Lat-Vent, . +/- .
as100351_conv Left-Inf-Lat-Vent value .025678500 is an outlier (avg = .
+/- .)...
checking subcortical label: 

Re: [Freesurfer] QA Tools Snaps Scrambled - Follow up

[Louis Nicholas Vinke]

Hi Wil,
Well the workaround is to use the SaveTIFF command instead of the SaveRGB 
command in the tcl script which QATools uses for tkmedit snapshots.  There 
are a couple lines in the shell scripts that needs to be changed as well. 
Which version of the QATools do you have 1.1?

-Louis

On Thu, 10 Jan 2013, Irwin, William wrote:


Hi Louis-

I dug a little deeper and examined the rgb files before conversion. The problem is 
not with the IM conversion, it is with the capture. For example, 
'subject_curv_lh_lat.rgb' is just fine, but from the same subject 
'snapshot-talairach-H-128.rgb' is garbage.

Any ideas on this?

Thanks,
Wil

-Original Message-
From: Irwin, William
Sent: Wednesday, January 09, 2013 6:22 AM
To: Louis Nicholas Vinke
Cc: freesurfer@nmr.mgh.harvard.edu; Irwin, William
Subject: RE: [Freesurfer] QA Tools Snaps Scrambled - Clairification

Hi Louis-

I was speaking cryptically and/or imprecisely. Of course there are dependencies 
for IM-- in fact about 8 libraries which are uniquely required by IM. I was 
thinking about a higher (or lower) level of dependency. This would suggest a 
more system-level problem, but I'm not having problems with any of the other 
apps running on my system. Obviously I'm not asking you to help diagnose the 
health of my system, but though you might have some thoughts/suggestions.

Regards,
Wil

-Original Message-
From: Irwin, William
Sent: Wednesday, January 09, 2013 5:37 AM
To: Louis Nicholas Vinke
Cc: freesurfer@nmr.mgh.harvard.edu; Irwin, William
Subject: RE: [Freesurfer] QA Tools Snaps Scrambled

Hi Louis-

No problem doing command line conversion of an rgb to either jpg or gif in 
terms of error messages. However, the converted files are scrambled. Might 
there be a dependency on which ImageMagick relies which still in place, but 
corrupted? I was under the impression ImageMagick was self-contained.

This is a real mystery

-Wil

-Original Message-
From: Louis Nicholas Vinke [mailto:vi...@nmr.mgh.harvard.edu]
Sent: Tuesday, January 08, 2013 6:29 PM
To: Irwin, William
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] QA Tools Snaps Scrambled

Hi Irwin,
It sounds like the snapshots from tksurfer are fine, but the ones from tkmedit 
are not being generated properly.  It may be this peculiar bug where 
ImageMagick has trouble reading rgb files. Try converting an rgb file to a jpg 
'convert file.rgb file.jpg'.  You may get the error 'Improper image header'.  
The tksurfer tcl script saves tiff files, the tkmedit tcl script saves rgbs, 
which may explain why some images are fine.
-Louis

On Tue, 8 Jan 2013, Irwin, William wrote:



Hi-

 

I’ve come across a peculiar behavior with recon_checker, and am hoping
someone can shed some light on this.

 

I have used it 100’s of times in the past, but not for about 2 months.
I recently processed a large set of cases I wanted to QC. When I ran
it, some, but not all, of the snaps were corrupted. Specifically the
talairach, aseg, surfs, and all the ‘detailed snaps’, which are
basically additional instances of the aforementioned types. The
inflated, curv, and parc are all just fine. As the process runs, all
images are being displayed in the pop-up windows, and the html page is created.

 

While there have been no system changes which should affect this, I
upgraded from ImageMagick 6.5.4 to 6.8.1 to see if this would fix the
problem. The problem remains. And the problem remains w/ or w/o the
flag for detailed snaps.

 

If all of the images were corrupted, I would have certainly concluded
something has gone awry with my system. The fact that only some of the
images are corrupted makes me scratch my head.

 

Thoughts? Suggestions?

 

Thanks,

Wil






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Re: [Freesurfer] QA Tools Snaps Scrambled - Follow up

[Irwin, William]

Hi Louis-

I dug a little deeper and examined the rgb files before conversion. The problem 
is not with the IM conversion, it is with the capture. For example, 
'subject_curv_lh_lat.rgb' is just fine, but from the same subject 
'snapshot-talairach-H-128.rgb' is garbage.

Any ideas on this?

Thanks,
Wil

-Original Message-
From: Irwin, William 
Sent: Wednesday, January 09, 2013 6:22 AM
To: Louis Nicholas Vinke
Cc: freesurfer@nmr.mgh.harvard.edu; Irwin, William
Subject: RE: [Freesurfer] QA Tools Snaps Scrambled - Clairification

Hi Louis-

I was speaking cryptically and/or imprecisely. Of course there are dependencies 
for IM-- in fact about 8 libraries which are uniquely required by IM. I was 
thinking about a higher (or lower) level of dependency. This would suggest a 
more system-level problem, but I'm not having problems with any of the other 
apps running on my system. Obviously I'm not asking you to help diagnose the 
health of my system, but though you might have some thoughts/suggestions.

Regards,
Wil

-Original Message-
From: Irwin, William
Sent: Wednesday, January 09, 2013 5:37 AM
To: Louis Nicholas Vinke
Cc: freesurfer@nmr.mgh.harvard.edu; Irwin, William
Subject: RE: [Freesurfer] QA Tools Snaps Scrambled

Hi Louis-

No problem doing command line conversion of an rgb to either jpg or gif in 
terms of error messages. However, the converted files are scrambled. Might 
there be a dependency on which ImageMagick relies which still in place, but 
corrupted? I was under the impression ImageMagick was self-contained.

This is a real mystery

-Wil

-Original Message-
From: Louis Nicholas Vinke [mailto:vi...@nmr.mgh.harvard.edu]
Sent: Tuesday, January 08, 2013 6:29 PM
To: Irwin, William
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] QA Tools Snaps Scrambled

Hi Irwin,
It sounds like the snapshots from tksurfer are fine, but the ones from tkmedit 
are not being generated properly.  It may be this peculiar bug where 
ImageMagick has trouble reading rgb files. Try converting an rgb file to a jpg 
'convert file.rgb file.jpg'.  You may get the error 'Improper image header'.  
The tksurfer tcl script saves tiff files, the tkmedit tcl script saves rgbs, 
which may explain why some images are fine.
-Louis

On Tue, 8 Jan 2013, Irwin, William wrote:

 
 Hi-
 
  
 
 I’ve come across a peculiar behavior with recon_checker, and am hoping 
 someone can shed some light on this.
 
  
 
 I have used it 100’s of times in the past, but not for about 2 months. 
 I recently processed a large set of cases I wanted to QC. When I ran 
 it, some, but not all, of the snaps were corrupted. Specifically the 
 talairach, aseg, surfs, and all the ‘detailed snaps’, which are 
 basically additional instances of the aforementioned types. The 
 inflated, curv, and parc are all just fine. As the process runs, all 
 images are being displayed in the pop-up windows, and the html page is 
 created.
 
  
 
 While there have been no system changes which should affect this, I 
 upgraded from ImageMagick 6.5.4 to 6.8.1 to see if this would fix the 
 problem. The problem remains. And the problem remains w/ or w/o the 
 flag for detailed snaps.
 
  
 
 If all of the images were corrupted, I would have certainly concluded 
 something has gone awry with my system. The fact that only some of the 
 images are corrupted makes me scratch my head.
 
  
 
 Thoughts? Suggestions?
 
  
 
 Thanks,
 
 Wil
 
 



The information in this e-mail is intended only for the person to whom it is 
addressed. If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Partners Compliance HelpLine 
at http://www.partners.org/complianceline . If the e-mail was sent to you in 
error but does not contain patient information, please contact the sender and 
properly dispose of the e-mail.


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Re: [Freesurfer] QA Tools Snaps Scrambled

[Irwin, William]

Hi Louis-

No problem doing command line conversion of an rgb to either jpg or gif in 
terms of error messages. However, the converted files are scrambled. Might 
there be a dependency on which ImageMagick relies which still in place, but 
corrupted? I was under the impression ImageMagick was self-contained.

This is a real mystery

-Wil

-Original Message-
From: Louis Nicholas Vinke [mailto:vi...@nmr.mgh.harvard.edu] 
Sent: Tuesday, January 08, 2013 6:29 PM
To: Irwin, William
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] QA Tools Snaps Scrambled

Hi Irwin,
It sounds like the snapshots from tksurfer are fine, but the ones from tkmedit 
are not being generated properly.  It may be this peculiar bug where 
ImageMagick has trouble reading rgb files. Try converting an rgb file to a jpg 
'convert file.rgb file.jpg'.  You may get the error 'Improper image header'.  
The tksurfer tcl script saves tiff files, the tkmedit tcl script saves rgbs, 
which may explain why some images are fine.
-Louis

On Tue, 8 Jan 2013, Irwin, William wrote:

 
 Hi-
 
  
 
 I’ve come across a peculiar behavior with recon_checker, and am hoping 
 someone can shed some light on this.
 
  
 
 I have used it 100’s of times in the past, but not for about 2 months. 
 I recently processed a large set of cases I wanted to QC. When I ran 
 it, some, but not all, of the snaps were corrupted. Specifically the 
 talairach, aseg, surfs, and all the ‘detailed snaps’, which are 
 basically additional instances of the aforementioned types. The  
 inflated, curv, and parc are all just fine. As the process runs, all 
 images are being displayed in the pop-up windows, and the html page is 
 created.
 
  
 
 While there have been no system changes which should affect this, I 
 upgraded from ImageMagick 6.5.4 to 6.8.1 to see if this would fix the 
 problem. The problem remains. And the problem remains w/ or w/o the 
 flag for detailed snaps.
 
  
 
 If all of the images were corrupted, I would have certainly concluded 
 something has gone awry with my system. The fact that only some of the 
 images are corrupted makes me scratch my head.
 
  
 
 Thoughts? Suggestions?
 
  
 
 Thanks,
 
 Wil
 
 



The information in this e-mail is intended only for the person to whom it is 
addressed. If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Partners Compliance HelpLine 
at http://www.partners.org/complianceline . If the e-mail was sent to you in 
error but does not contain patient information, please contact the sender and 
properly dispose of the e-mail.


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Re: [Freesurfer] QA Tools Snaps Scrambled - Clairification

[Irwin, William]

Hi Louis-

I was speaking cryptically and/or imprecisely. Of course there are dependencies 
for IM-- in fact about 8 libraries which are uniquely required by IM. I was 
thinking about a higher (or lower) level of dependency. This would suggest a 
more system-level problem, but I'm not having problems with any of the other 
apps running on my system. Obviously I'm not asking you to help diagnose the 
health of my system, but though you might have some thoughts/suggestions.

Regards,
Wil

-Original Message-
From: Irwin, William 
Sent: Wednesday, January 09, 2013 5:37 AM
To: Louis Nicholas Vinke
Cc: freesurfer@nmr.mgh.harvard.edu; Irwin, William
Subject: RE: [Freesurfer] QA Tools Snaps Scrambled

Hi Louis-

No problem doing command line conversion of an rgb to either jpg or gif in 
terms of error messages. However, the converted files are scrambled. Might 
there be a dependency on which ImageMagick relies which still in place, but 
corrupted? I was under the impression ImageMagick was self-contained.

This is a real mystery

-Wil

-Original Message-
From: Louis Nicholas Vinke [mailto:vi...@nmr.mgh.harvard.edu]
Sent: Tuesday, January 08, 2013 6:29 PM
To: Irwin, William
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] QA Tools Snaps Scrambled

Hi Irwin,
It sounds like the snapshots from tksurfer are fine, but the ones from tkmedit 
are not being generated properly.  It may be this peculiar bug where 
ImageMagick has trouble reading rgb files. Try converting an rgb file to a jpg 
'convert file.rgb file.jpg'.  You may get the error 'Improper image header'.  
The tksurfer tcl script saves tiff files, the tkmedit tcl script saves rgbs, 
which may explain why some images are fine.
-Louis

On Tue, 8 Jan 2013, Irwin, William wrote:

 
 Hi-
 
  
 
 I’ve come across a peculiar behavior with recon_checker, and am hoping 
 someone can shed some light on this.
 
  
 
 I have used it 100’s of times in the past, but not for about 2 months. 
 I recently processed a large set of cases I wanted to QC. When I ran 
 it, some, but not all, of the snaps were corrupted. Specifically the 
 talairach, aseg, surfs, and all the ‘detailed snaps’, which are 
 basically additional instances of the aforementioned types. The 
 inflated, curv, and parc are all just fine. As the process runs, all 
 images are being displayed in the pop-up windows, and the html page is 
 created.
 
  
 
 While there have been no system changes which should affect this, I 
 upgraded from ImageMagick 6.5.4 to 6.8.1 to see if this would fix the 
 problem. The problem remains. And the problem remains w/ or w/o the 
 flag for detailed snaps.
 
  
 
 If all of the images were corrupted, I would have certainly concluded 
 something has gone awry with my system. The fact that only some of the 
 images are corrupted makes me scratch my head.
 
  
 
 Thoughts? Suggestions?
 
  
 
 Thanks,
 
 Wil
 
 



The information in this e-mail is intended only for the person to whom it is 
addressed. If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Partners Compliance HelpLine 
at http://www.partners.org/complianceline . If the e-mail was sent to you in 
error but does not contain patient information, please contact the sender and 
properly dispose of the e-mail.


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[Freesurfer] QA Tools Snaps Scrambled

[Irwin, William]

Hi-

I've come across a peculiar behavior with recon_checker, and am hoping someone 
can shed some light on this.

I have used it 100's of times in the past, but not for about 2 months. I 
recently processed a large set of cases I wanted to QC. When I ran it, some, 
but not all, of the snaps were corrupted. Specifically the talairach, aseg, 
surfs, and all the 'detailed snaps', which are basically additional instances 
of the aforementioned types. The  inflated, curv, and parc are all just fine. 
As the process runs, all images are being displayed in the pop-up windows, and 
the html page is created.

While there have been no system changes which should affect this, I upgraded 
from ImageMagick 6.5.4 to 6.8.1 to see if this would fix the problem. The 
problem remains. And the problem remains w/ or w/o the flag for detailed snaps.

If all of the images were corrupted, I would have certainly concluded something 
has gone awry with my system. The fact that only some of the images are 
corrupted makes me scratch my head.

Thoughts? Suggestions?

Thanks,
Wil
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] QA Tools Snaps Scrambled

[Louis Nicholas Vinke]

Hi Irwin,
It sounds like the snapshots from tksurfer are fine, but the ones from 
tkmedit are not being generated properly.  It may be this peculiar bug 
where ImageMagick has trouble reading rgb files. Try converting an rgb 
file to a jpg 'convert file.rgb file.jpg'.  You may get the error 
'Improper image header'.  The tksurfer tcl script saves tiff files, the 
tkmedit tcl script saves rgbs, which may explain why some images are fine.

-Louis

On Tue, 8 Jan 2013, Irwin, William wrote:



Hi-

 

I’ve come across a peculiar behavior with recon_checker, and am hoping
someone can shed some light on this.

 

I have used it 100’s of times in the past, but not for about 2 months. I
recently processed a large set of cases I wanted to QC. When I ran it, some,
but not all, of the snaps were corrupted. Specifically the talairach, aseg,
surfs, and all the ‘detailed snaps’, which are basically additional
instances of the aforementioned types. The  inflated, curv, and parc are all
just fine. As the process runs, all images are being displayed in the pop-up
windows, and the html page is created.

 

While there have been no system changes which should affect this, I upgraded
from ImageMagick 6.5.4 to 6.8.1 to see if this would fix the problem. The
problem remains. And the problem remains w/ or w/o the flag for detailed
snaps.

 

If all of the images were corrupted, I would have certainly concluded
something has gone awry with my system. The fact that only some of the
images are corrupted makes me scratch my head.

 

Thoughts? Suggestions?

 

Thanks,

Wil


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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] QA tools--Permission denied??

[Jenni Pacheco]

Hi,

We had never really finalized the QA Tools to feel comfortable distributing
them, and so the permissions on these files are still set so that only the
group of us working with them can use it.  In fact, I had thought that the
wiki page associated with it was likewise only available to those same
people (to avoid this exact confusion).  Our goal had been to incorporate
these scripts into the FS distribution, but that hasn't happened yet.  I'm
no longer at the center, but I'm sure someone else can give you access to
these - if you copy it to your own directory (i.e., don't use our only copy
of the scripts).

Thanks,
Jenni

On 10/9/07, Pratap Kunwar [EMAIL PROTECTED] wrote:

 hi all

 I tried to use QA tools on the wiki (writen by jpacheco) at

 https://surfer.nmr.mgh.harvard.edu/fswiki/QATools?action=highlightvalue=qa+tools
 .

 I got the following error saying permission denied. I could not even copy
 the QATOOLS to my folder.

 thanks
 pratap

 [galen:S4_HR_LR18_recon] (nmr-std-env) setenv QA_SCRIPTS
 /space/tensor/17/users/jpacheco/QAtools [galen:S4_HR_LR18_recon]
 (nmr-std-env) $QA_SCRIPTS/data_checker/recon_checker -nocheckasegoutliers
 -s rfa1410 -o QAsnap.html
 /space/tensor/17/users/jpacheco/QAtools/data_checker/recon_checker:
 Permission denied.

 --
 FREESURFER_HOME: /usr/local/freesurfer/stable4
 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.0.1-20071006
 RedHat release: CentOS release 4.4 (Final)
 Kernel info: Linux 2.6.9-42.0.3.ELsmp x86_64
 NMR Center info (/space/freesurfer exists):
   machine: galen
   SUBJECTS_DIR:
 /autofs/space/galen_002/users/carl/S4_HR_LR18/S4_HR_LR18_recon/
   PWD: /space/galen/2/users/carl/S4_HR_LR18/S4_HR_LR18_recon


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-- 
Jenni Pacheco, MA
Learning and Memory Lab
The University of Texas at Austin
Department of Psychology
1 University Station A8000
Austin, TX 78712
phone: (512) 471-2727
fax: (512) 471-5935
email: [EMAIL PROTECTED]
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