Edit the number of segments in the segmentation of the corpus callosum

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UQAM

23 Nov 2015 23 Nov '15

8:24 a.m.

Hi,

This a a "re-posting" of a question I've raised last week ; )

I would like to segment the corpus callosum into *twelve* even lenght segments instead of the five segments that freesurfer includes by default.

- First I ran a mri_cc on subject e0070:

mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.12segmentsCC.mgz -d 12 e0070

- Then I edited the ColorLUT.txt file and renamed it CColorLUT.txt (see attachment, segments 251 to 262).

- Finally I ran a mri_segstats to compute the statistics on segmented volumes.

mri_segstats seg $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz --ctab $SUBJECTS_DIR/CColorLUT.txt --nonempty --excludeid 0 sum --e0070_CC12.aseg.stats

The e0070_CC12.aseg.stats file still displays only five segments of the corpus callosum.

Any tips or clues on how I could do things differently to get 12 segments?

Thanks in advance,

Geneviève

Attachments:

attachment.html (text/html — 1.8 KB)
CColorLUT.txt (text/plain — 83.1 KB)
e0070_CC12.aseg.stats (application/octet-stream — 4.0 KB)
aseg.12segmentsCC.mgz (application/octet-stream — 205.7 KB)

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Bruce Fischl

23 Nov 23 Nov

8:39 a.m.

Hi Geneviève

if you send us the $SUBJECTS_DIR/CColorLUT.txt and $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz and we will take a look

cheers Bruce On Mon, 23 Nov 2015, UQAM wrote:

...

Hi, This a a "re-posting" of a question I've raised last week ; )

I would like to segment the corpus callosum into twelve even lenght segments instead of the five segments that freesurfer includes by default.

First I ran a mri_cc on subject e0070:

mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.12segmentsCC.mgz -d 12 e0070

Then I edited the ColorLUT.txt file and renamed it CColorLUT.txt (see

attachment, segments 251 to 262).

Finally I ran a mri_segstats to compute the statistics on segmented

volumes.

mri_segstats seg $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz --ctab $SUBJECTS_DIR/CColorLUT.txt --nonempty --excludeid 0 sum --e0070_CC12.aseg.stats

The e0070_CC12.aseg.stats file still displays only five segments of the corpus callosum.

Any tips or clues on how I could do things differently to get 12 segments?

Thanks in advance,

Geneviève

UQAM

10:21 a.m.

New subject: Edit the number of segments in the segmentation of the corpus callosum

Hi Bruce,

Please find the two files attached.

Genevieve

On Mon, Nov 23, 2015 at 2:39 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

...

Hi Geneviève

if you send us the $SUBJECTS_DIR/CColorLUT.txt and $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz and we will take a look

cheers Bruce

On Mon, 23 Nov 2015, UQAM wrote:

Hi,

...
This a a "re-posting" of a question I've raised last week ; )

I would like to segment the corpus callosum into twelve even lenght segments instead of the five segments that freesurfer includes by default.

First I ran a mri_cc on subject e0070:

mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.12segmentsCC.mgz -d 12 e0070

Then I edited the ColorLUT.txt file and renamed it CColorLUT.txt (see

attachment, segments 251 to 262).

Finally I ran a mri_segstats to compute the statistics on segmented

volumes.

mri_segstats seg $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz --ctab $SUBJECTS_DIR/CColorLUT.txt --nonempty --excludeid 0 sum --e0070_CC12.aseg.stats

The e0070_CC12.aseg.stats file still displays only five segments of the corpus callosum.

Any tips or clues on how I could do things differently to get 12 segments?

Thanks in advance,

Geneviève

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

angela.favaro＠unipd.it

12:16 p.m.

New subject: QA tools

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

Harms, Michael

6:10 p.m.

New subject: QA tools

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: mharms@wustl.edu

On 11/23/15 11:16 AM, "angela.favaro@unipd.it" angela.favaro@unipd.it wrote:

Hi all,

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

Thank you for any help you can give me

Best wishes

Angela

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

________________________________ 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.

Bruce Fischl

6:59 p.m.

New subject: QA tools

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: mharms@wustl.edu

On 11/23/15 11:16 AM, "angela.favaro@unipd.it" angela.favaro@unipd.it wrote:

Hi all,

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

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?

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

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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.

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

angela.favaro＠unipd.it

24 Nov 24 Nov

5:24 a.m.

New subject: QA tools

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: mharms@wustl.edu

On 11/23/15 11:16 AM, "angela.favaro@unipd.it" angela.favaro@unipd.it wrote:

Hi all,

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

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?

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

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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.

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Bruce Fischl

23 Nov 23 Nov

1:32 p.m.

New subject: Edit the number of segments in the segmentation of the corpus callosum

Hi Genevieve

I just tracked this down and it is a bug in mri_cc. If you tell Zeke your hardware/software environment he can get you a new version that should work cheers Bruce

On Mon, 23 Nov 2015, UQAM wrote:

...

Hi Bruce, Please find the two files attached.

Genevieve

On Mon, Nov 23, 2015 at 2:39 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Geneviève
  if you send us the $SUBJECTS_DIR/CColorLUT.txt and $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz and we will take a
  look

  cheers
  Bruce
  On Mon, 23 Nov 2015, UQAM wrote:

        Hi,
        This a a "re-posting" of a question I've raised last week ; )

        I would like to segment the corpus callosum into twelve even lenght segments
        instead of the five segments that freesurfer includes by default.

        - First I ran a mri_cc on subject e0070: 

        mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.12segmentsCC.mgz -d 12 e0070

        - Then I edited the ColorLUT.txt file and renamed it CColorLUT.txt (see
        attachment, segments 251 to 262).

        - Finally I ran a mri_segstats to compute the statistics on segmented
        volumes. 

        mri_segstats seg $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz --ctab
        $SUBJECTS_DIR/CColorLUT.txt --nonempty --excludeid 0 sum
        --e0070_CC12.aseg.stats

        The e0070_CC12.aseg.stats file still displays only five segments of the
        corpus callosum.

        Any tips or clues on how I could do things differently to get 12 segments?

        Thanks in advance,

        Geneviève
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

UQAM

24 Nov 24 Nov

5:56 a.m.

New subject: Edit the number of segments in the segmentation of the corpus callosum

Hi Bruce,

DELL R910 Intel(R) Xeon(R) CPU E7520 @ 1.87GHz (16 cores) 32 Go RAM CentOS release 5.10 (Final) kernel 2.6.18-371.3.1.el5

On Mon, Nov 23, 2015 at 7:32 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

...

Hi Genevieve

I just tracked this down and it is a bug in mri_cc. If you tell Zeke your hardware/software environment he can get you a new version that should work

cheers Bruce

On Mon, 23 Nov 2015, UQAM wrote:

Hi Bruce,

...
Please find the two files attached.

Genevieve

On Mon, Nov 23, 2015 at 2:39 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Geneviève
  if you send us the $SUBJECTS_DIR/CColorLUT.txt and
$SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz and we will take a look
  cheers
  Bruce
  On Mon, 23 Nov 2015, UQAM wrote:

        Hi,
        This a a "re-posting" of a question I've raised last week ; )

        I would like to segment the corpus callosum into twelve even
lenght segments instead of the five segments that freesurfer includes by default.
        - First I ran a mri_cc on subject e0070:

        mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.12segmentsCC.mgz
-d 12 e0070
        - Then I edited the ColorLUT.txt file and renamed it
CColorLUT.txt (see attachment, segments 251 to 262).
        - Finally I ran a mri_segstats to compute the statistics on
segmented volumes.
        mri_segstats seg
$SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz --ctab $SUBJECTS_DIR/CColorLUT.txt --nonempty --excludeid 0 sum --e0070_CC12.aseg.stats
        The e0070_CC12.aseg.stats file still displays only five
segments of the corpus callosum.
        Any tips or clues on how I could do things differently to get
12 segments?
        Thanks in advance,

        Geneviève
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

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angela.favaro＠unipd.it
Bruce Fischl
Harms, Michael
UQAM