Hi Doug,

 

Sorry I am a bit confused. I ran recon-all as a bash for 30 participants. None of which had the right hemisphere completed and recon-all log says exited with errors (as the log in the original email shows). Are you suggesting I go back and re-run recon-all via the bash and see if I get the same issue?

 

Thanks for all your help.

Mason

 

 

 

It looks like that command finished without error. Have you tried running it in recon-all again to see if it fails again? You can just run that command with -parcstats3

        External Email - Use Caution        

Hi Doug,

 

Not sure if my email below got to you? I sent the terminal outputs of the command you told me to run. Any idea what’s going on or how to fix it?

 

Cheers,

Mason

 

Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff    CF24 4HQ UK   Email: WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpage

Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd    CF24 4HQ  DU   E-bost: WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

 

 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Mason Wells <WellsMT1@cardiff.ac.uk>
Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, 4 May 2020 at 20:01
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all exited WITH errors {Disarmed}

 

        External Email - Use Caution        

Ah yes. I just set the SUBJECTS_DIR correctly, Terminal out below:

 

mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab PPT_001 lh white

INFO: assuming MGZ format for volumes.

INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.

computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot.

reading volume /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/mri/wm.mgz...

reading input surface /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/surf/lh.white...

reading input pial surface /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/surf/lh.pial...

reading input white surface /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/surf/lh.white...

reading colortable from annotation file...

colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt)

Saving annotation colortable ../label/aparc.annot.DKTatlas40.ctab

 

table columns are:

    number of vertices

    total surface area (mm^2)

    total gray matter volume (mm^3)

    average cortical thickness +- standard deviation (mm)

    integrated rectified mean curvature

    integrated rectified Gaussian curvature

    folding index

    intrinsic curvature index

    structure name

 

1698   1132   3274  2.730 0.526     0.130     0.032       26     2.4  caudalanteriorcingulate

4375   2908   8369  2.594 0.599     0.127     0.040       46     7.0  caudalmiddlefrontal

3883   2464   5378  2.087 0.498     0.149     0.082       74     9.4  cuneus

  546    373   1423  2.817 0.999     0.154     0.087       11     1.9  entorhinal

5411   3506  10979  2.768 0.567     0.137     0.059      101    14.8  fusiform

6159   4159  11629  2.543 0.520     0.133     0.045       86    11.0  inferiorparietal

5973   3945  13736  2.965 0.705     0.138     0.060      130    13.4  inferiortemporal

1536    934   2788  2.725 0.838     0.164     0.090       50     5.1  isthmuscingulate

6953   4476  11030  2.320 0.542     0.147     0.055      110    15.3  lateraloccipital

3897   2512   7780  2.641 0.630     0.147     0.077       99    13.1  lateralorbitofrontal

5273   3237   7567  2.161 0.603     0.151     0.956      191    20.8  lingual

2015   1290   4210  2.576 0.773     0.157     0.084       64     6.5  medialorbitofrontal

6073   4091  14456  3.026 0.553     0.130     0.043       80    11.0  middletemporal

1012    711   2254  2.886 0.735     0.133     0.112       16     6.3  parahippocampal

2182   1401   4296  2.690 0.669     0.128     0.044       26     4.5  paracentral

3247   2175   6722  2.682 0.501     0.121     0.038       34     5.1  parsopercularis

1195    793   2520  2.549 0.514     0.138     0.045       21     2.1  parsorbitalis

2780   1882   5377  2.457 0.608     0.131     0.043       37     5.0  parstriangularis

2229   1444   2359  1.685 0.476     0.155     0.067       41     6.1  pericalcarine

7692   4818  11728  2.218 0.657     0.130     0.053      114    16.0  postcentral

1983   1360   4109  2.902 0.617     0.167     0.079       44     6.1  posteriorcingulate

7681   4765  13220  2.521 0.549     0.123     0.056      119    15.1  precentral

6240   4189  11573  2.532 0.576     0.145     0.052      104    13.3  precuneus

1613    992   3166  2.820 0.661     0.136     0.055       54     3.6  rostralanteriorcingulate

6644   4495  12118  2.347 0.579     0.144     0.052      117    13.9  rostralmiddlefrontal

12967   8768  28469  2.839 0.612     0.132     0.047      170    25.1  superiorfrontal

7963   5213  12201  2.095 0.481     0.125     0.053      125    16.2  superiorparietal

9021   6069  20753  3.059 0.612     0.130     0.050      183    19.9  superiortemporal

7970   5269  15543  2.684 0.502     0.149     0.074      910    17.4  supramarginal

  702    454   1432  2.844 0.618     0.133     0.046        8     1.3  transversetemporal

2953   1947   6539  3.228 0.801     0.124     0.056       33     6.4  insula

 

Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff    CF24 4HQ UK   Email: WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpage

Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd    CF24 4HQ  DU   E-bost: WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

 

 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, 4 May 2020 at 19:56
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all exited WITH errors {Disarmed}

 

Something else has gone wrong. wm.mgz should have been there in order to get as far as it did. Is your SUBJECTS_DIR set properly?

On 5/4/2020 2:49 PM, Mason Wells wrote:

        External Email - Use Caution        

Hi,

 

Terminal output is below:

 

/Documents/Analysis/Data/freesurfer/subjects/PPT_001/scripts$ mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab PPT_001 lh white

INFO: assuming MGZ format for volumes.

INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.

computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot.

reading volume /cubric/data/c1749990/freesurfer/subjects/PPT_001/mri/wm.mgz...

mghRead(/cubric/data/c1749990/freesurfer/subjects/PPT_001/mri/wm.mgz, -1): could not open file

mris_anatomical_stats: could not read input volume /cubric/data/c1749990/freesurfer/subjects/PPT_001/mri/wm.mgz

 

Cheers,

Mason

 

Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff    CF24 4HQ UK   Email: WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpage

Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd    CF24 4HQ  DU   E-bost: WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

 

 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, 4 May 2020 at 18:54
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all exited WITH errors

 

Unfortunately, the log file does not indicate what went wrong. But it does show that the error happened on the LH (so it is not just RH). Run the command below and send all terminal output

cd /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/scripts
 mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab PPT_001 lh white

On 5/4/2020 1:34 PM, Mason Wells wrote:

        External Email - Use Caution        

Hi Experts,

 

I appear to be having some issues with recon-all. I ran the command from a bash script (see attached), and it appears to work fine for the left hemisphere as the correct files are in the surf folder. However, there are no right hemisphere surf files. I have attached the log and error log for PPT01 and PPT02. Any advice on as to why this has happened would be great.

 

Thanks in advance,

Mason

 

Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff    CF24 4HQ UK   Email: WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpage

Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd    CF24 4HQ  DU   E-bost: WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

 

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