Hi April

what version are you using and what operating system? There was a bug that caused holes in labels that we fixed not that long ago.

cheers Bruce

On Sat, 2 Aug 2014, April Clausen wrote:

The command line for mapping the labels from fsaverage to the subject (april) was,

mri_label2label —srcsubject fsaverage —srclabel rh.aprilOne.label —trgsubject april —trglabel rh.aprilOne.label —hemi rh —regmethod surface

this was repeated 5 more times for labels rh.aprilTwo.label to rh.aprilSix.label

The command line for creating the annot file on the subject (april) was

mris_label2annot —s april —h rh —ctab april.annot.ctab —a rh.april —l rh.aprilOne.label —l rh.aprilTwo.label —l rh.aprilThree.label —l rh.aprilFour.label —l rh.aprilFive.label —l rh.aprilSix.label

We initially defined the label using tksurfer on the pial surface to utilize the fold lines to define the regions. We then ran through the above process and found that the regions were showing substantial holes. We then tried redefining the regions on the inflated surface of fsaverage using tksurfer (calling the labels back in on the inflated surface, tracing the outlines and re-saving). We repeated the mapping and annot file creation and this substantially reduced the number of holes in the regions mapped onto our subjects but holes were still present (as shown in previous images).

April On Aug 1, 2014, at 4:12 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

...

what was your command line?

On 07/21/2014 03:43 PM, April Clausen wrote:

...

Hi Dr. Greve, I tried to upload the images with the Martinos Centre Dropbox but I could not activate the dropbox … so the images are attached. The 6 labels and annot file were created on fsaverage and the image shows no holes in the regions. The 6 labels were mapped to a subject and an annot file was created … the subject files shows holes in the regions.

April Clausen

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Hi Angela,

Use mris_euler_number on the pial surface, but the probability that there will be any defect is indeed relatively low. Have you carefully checked your white and pial surface slice by slice overlaid on the T1? Sometimes a small region where the surfaces are "wrinkled" is responsible for this error. If this is the case, edit the wm and rerun autorecon2-wm and autorecon3. If this is not the case, i.e. if you don't see anything to edit in the wm, then the best solution is to rerun autorecon2-wm and autorecon3 with the randomness flag. That should solve the issue.

As for your second question, if this is the same subject than the one you got the error, the solution above should solve it. If not, I would advise reprocessing it.

Hope it helps,

Marie

On Aug 3, 2014, at 9:28 AM, angela.favaro@unipd.it wrote:

Hi all, I am running lgi analyses in 5.3 FS version (lion OSX)

one of my subjects failed with a typical message:

lGI for vertex number 39901 of the outer mesh is 1.8067 ... remeasuring lGI value for vertex iV = 40001. It may take a few minutes. WARNING -- Problem for vertex iV = 40001, lGI value is aberrantly high (lGI=42.8793)... ...lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface.

Before running again the command mris_compute_lgi I want to check for the presence of topological defects

I have some questions:

1. which is the command line for the command mris_euler_number or - better

• which are the surface files to control for? (lh.orig, lh.pial, lh.white,

etc...)

2. I have performed the command check_subject and in all my subjects

appear this message:

[host-001:~/Desktop/risonanze/studyfree] angelafavaro% check_subject subj061 CHECKING SUBJECT subj061 WARN: time for rh.white is older than rh.inflated WARN: lh.rh.sphere.reg is empty/missing WARN: time for lh.white is older than lh.inflated

What is the problem (if any)?

Thank you for any help

Angela

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________________________________________ Hello Tracula Experts,

I noticed that for a few of my subjects, I am missing all "Center" statistics for FA, MD etc. for certain tracts like the left uncinate fasciculus for example.

I am assuming this means that an optimal pathway was unable to be found? I do have the average and weighted statistics for these subjects. Should I consider excluding these subjects or should I try analyzing them again with different parameters?

Additionally, I noticed that for a couple of my subjects, the "Length Center" (length of the highest probability pathway) is unusually short compared to the rest of the subjects? Is this a problem and do I consider excluding or tweaking the parameters for these subjects?

Also, do individuals usually report in publications just the average statistics or are the weighted average or center statistics used?

Attached are the stats of the problematic subjects. Any advice would be greatly appreciated!

Emily

Hi Bruce, hi Maria, thank you for your suggestions!

However, the message WARN: time for rh.white is older than rh.inflated WARN: lh.rh.sphere.reg is empty/missing WARN: time for lh.white is older than lh.inflated

appears for all subjects I checked.

I tried with the command: recon-all -s <subject> -sd <subjects_dir> -make all

but give me (again for all subjects):

Subject 'subj061': make all make: Nothing to be done for `all'.

Is it something to worry about?

thank you Angela

Hi Angela

1. if recon-all has completed successfully there shouldn't be any

topological defects. You can run mris_euler_number on lh.pial and rh.pial. The Euler number for a closed surface with no defects should be 2.

2. This means something has been rerun but not to completion. You should

be able to run

recon-all -s <subject> -sd <subjects_dir> -make all

and it will rerun whatever it needs to

cheers Bruce

On Sun, 3 Aug 2014, angela.favaro@unipd.it wrote:

...

Hi all, I am running lgi analyses in 5.3 FS version (lion OSX)

one of my subjects failed with a typical message:

lGI for vertex number 39901 of the outer mesh is 1.8067 ... remeasuring lGI value for vertex iV = 40001. It may take a few minutes. WARNING -- Problem for vertex iV = 40001, lGI value is aberrantly high (lGI=42.8793)... ...lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface.

Before running again the command mris_compute_lgi I want to check for the presence of topological defects

I have some questions:

1. which is the command line for the command mris_euler_number or -

better

• which are the surface files to control for? (lh.orig, lh.pial,

lh.white, etc...)

2. I have performed the command check_subject and in all my subjects

appear this message:

[host-001:~/Desktop/risonanze/studyfree] angelafavaro% check_subject subj061 CHECKING SUBJECT subj061 WARN: time for rh.white is older than rh.inflated WARN: lh.rh.sphere.reg is empty/missing WARN: time for lh.white is older than lh.inflated

What is the problem (if any)?

Thank you for any help

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.