Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30127 discussions

stage1 error
by Lukas Pezawas 24 Mar '04

24 Mar '04

Hi everybody, I've been having a strange problem running stage1 of recon-all. The process finishes successfully when I select "Process Volume" from the GUI, but fails when I start the stage via terminal command (using the same brain). I would prefer using the terminal command because I've been told it is a more up-to-date version than the GUI command. The command I entered was "recon-all -stage1 -nomorphrgb -subjid test0317bTerm" and it appeared to terminate during intensity normalization. Below is the error log. Thanks. -Aaron- on Mar 22 15:09:11 EST 2004 /usr/local/freesurfer_dev/bin/noarch/recon-all -stage1 -nomorphrgb -subjid test0317bTerm /j/freesurfsubj/test0317bTerm subjid test0317bTerm SUBJECTS_DIR /j/freesurfsubj FREESURFER_HOME /usr/local/freesurfer_dev Linux Filesystem 1K-blocks Used Available Use% Mounted on freud:/export/freesurfsubj 74697640 36308304 34594784 52% /j/freesurfsubj --------------------------------------------- MotionCor Mon Mar 22 15:09:12 EST 2004 INFO: no runs were found in /j/freesurfsubj/test0317bTerm/mri/orig/XXX, however, there is a volume in /j/freesurfsubj/test0317bTerm/mri/orig, so I am just going to proceed with that as the input. --------------------------------------------- Talairach Mon Mar 22 15:09:14 EST 2004 /j/freesurfsubj/test0317bTerm/mri talairach2 test0317bTerm INFO: registering test0317bTerm Mon Mar 22 15:09:14 EST 2004 -------------------------------------------- mri_convert orig orig/orig.mnc mri_convert orig orig/orig.mnc reading from orig... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to orig/orig.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -protocol icbm orig/orig.mnc transforms/talairach.xfm -------------------------------------------- mri_add_xform_to_header /j/freesurfsubj/test0317bTerm/mri/transforms/talairach.xfm /j/freesurfsubj/test0317bTerm/mri/orig /j/freesurfsubj/test0317bTerm/mri/orig Mon Mar 22 15:11:14 EST 2004 --------------------------------------------- Nu Intensity Correction Mon Mar 22 15:11:14 EST 2004 mri_convert orig nu/nu0.mnc mri_convert orig nu/nu0.mnc reading from orig... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to nu/nu0.mnc... nu_correct -clobber nu/nu0.mnc nu/nu1.mnc [goldmana@feynman:/j/freesurfsubj/test0317bTerm/mri/] [2004-03-22 15:11:32] running: /usr/local/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_21409/ nu/nu0.mnc nu/nu1.imp Processing:............................................................. .... Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 1 CV of field change: 2.16148e-26 [goldmana@feynman:/j/freesurfsubj/test0317bTerm/mri/] [2004-03-22 15:11:45] running: /usr/local/bin/make_template -quiet -shrink 3 nu/nu0.mnc /usr/tmp/nu_correct_21409//template.mnc Transforming slices:................................................................. .... .................Done 256+0 records in 256+0 records out Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:................................................................. .... ........................................................................ .... ........................................................................ .... ...................................Done nu_correct -clobber nu/nu1.mnc nu/nu2.mnc [goldmana@feynman:/j/freesurfsubj/test0317bTerm/mri/] [2004-03-22 15:12:16] running: /usr/local/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_21464/ nu/nu1.mnc nu/nu2.imp Processing:............................................................. .... Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 1 CV of field change: 3.04238e-26 [goldmana@feynman:/j/freesurfsubj/test0317bTerm/mri/] [2004-03-22 15:12:28] running: /usr/local/bin/make_template -quiet -shrink 3 nu/nu1.mnc /usr/tmp/nu_correct_21464//template.mnc Transforming slices:................................................................. .... .................Done 256+0 records in 256+0 records out Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:................................................................. .... ........................................................................ .... ........................................................................ .... ...................................Done nu_correct -clobber nu/nu2.mnc nu/nu3.mnc [goldmana@feynman:/j/freesurfsubj/test0317bTerm/mri/] [2004-03-22 15:12:59] running: /usr/local/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_21517/ nu/nu2.mnc nu/nu3.imp Processing:............................................................. .... Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 1 CV of field change: 2.0113e-26 [goldmana@feynman:/j/freesurfsubj/test0317bTerm/mri/] [2004-03-22 15:13:11] running: /usr/local/bin/make_template -quiet -shrink 3 nu/nu2.mnc /usr/tmp/nu_correct_21517//template.mnc Transforming slices:................................................................. .... .................Done 256+0 records in 256+0 records out Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:................................................................. .... ........................................................................ .... ........................................................................ .... ...................................Done nu_correct -clobber nu/nu3.mnc nu/nu4.mnc [goldmana@feynman:/j/freesurfsubj/test0317bTerm/mri/] [2004-03-22 15:13:43] running: /usr/local/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_21575/ nu/nu3.mnc nu/nu4.imp Processing:............................................................. .... Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 1 CV of field change: 2.08277e-26 [goldmana@feynman:/j/freesurfsubj/test0317bTerm/mri/] [2004-03-22 15:13:57] running: /usr/local/bin/make_template -quiet -shrink 3 nu/nu3.mnc /usr/tmp/nu_correct_21575//template.mnc Transforming slices:................................................................. .... .................Done 256+0 records in 256+0 records out Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:................................................................. .... ........................................................................ .... ........................................................................ .... ...................................Done mri_convert nu/nu4.mnc nu mri_convert nu/nu4.mnc nu reading from nu/nu4.mnc... DimSizes: 3, 256, 256, 256, 1 DataType: 1 MINC Linear Transform -1.0000 0.0000 0.0000 123.0000 0.0000 0.0000 1.0000 -122.3080 0.0000 -1.0000 0.0000 139.8577 0.0000 0.0000 0.0000 1.0000 Done reading minc TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions writing to nu... --------------------------------------------- Intensity Normalization Mon Mar 22 15:14:37 EST 2004 /j/freesurfsubj/test0317bTerm/mri mri_normalize orig T1 reading from orig... normalizing image... MRInormalize: could not find any valid peaks No such file or directory mri_normalize: normalization failed No such file or directory ERROR: mri_normalize exited with non-zero status ------------------------------------------ Filesystem 1K-blocks Used Available Use% Mounted on freud:/export/freesurfsubj 74697640 36325824 34577264 52% /j/freesurfsubj ------------------------------------------ recon-all exited with errors at Mon Mar 22 15:14:50 EST 2004

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create surface
by Bob Thoma 24 Mar '04

24 Mar '04

Hello all, I've had a problem with a few subjects. When I run Create Surface it fails at fill white matter. In the log file, it states, could not find corpus callosum. Then an alert states /home dir/<file name>/mri/filled/COR-001 .... not found ... wmfill first.. when you say ok, it says process interrupted, and closes. Anyone have any idea as to why it is failing, and what I can do to fix it?? Thanks Natalie _________________________________________________________________ Check out MSN PC Safety & Security to help ensure your PC is protected and safe. http://specials.msn.com/msn/security.asp

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Map_all_labels
by Keyma Prince 24 Mar '04

24 Mar '04

When map_all_labels is run is it using the average7 brain to know where to map the labels onto the surfaces? Also why are the labels (such as the central sulcus) generated by map_all_labels and parcellate_subject different? -Keyma Keyma Prince Massachusetts Institute of Technology Department of Brain and Cognitive Sciences NE20-392 Cambridge, MA 02139

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Detecting errors
by Satrajit Ghosh 22 Mar '04

22 Mar '04

Hi, Here is the output of lh.euler.orig for a particular subject: euler # = v-e+f = 2g-2: 149150 - 447444 + 298297 = 3 --> 0 holes F =2V-4: 298297 != 298300-4 (-1) 2E=3F: 894888 != 894891 (-3) total defect index = 4 Is there a way of determining which parts of the surface and therefore which parts of the volume are giving rising to the defects? It's likely I can write some surface analysis code to do this, but I'm hoping freesurfer already has something of this sort available. Thanks, Satra -- Satrajit S. Ghosh Department of Cognitive and Neural Systems, Boston University (I): http://www.cns.bu.edu/~satra

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looking at blocked data on a patch in surf-sess
by Stephanie McMains 19 Mar '04

19 Mar '04

I am trying to look at data analyzed as a block design on a flat.occip.patch. I am trying to use surf-sess to do this, but I have found if I set the patch option in the command line then it automatically thinks I am doing retinotopy and tries to use the twocond-flat.tcl script, which is incorrect. Is there a way to use surf-sess to view blocked design data on the patch? I just could not see a way. So I went in and edited the surf-sess script so that it did not automatically set the tcl script to twocond-flat.tcl when you used the -patch flag. I now have surf-sess setting the patch correctly, but in the end the inflated surface still comes up. Is there some way to override the inflated surface and get it to use the patch? An answer to either question would be most helpful! Thanks! Stephanie

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Re: mri_convert - use of hdr.hist.orient field incorrect
by Darren Weber 16 Mar '04

16 Mar '04

OK, so I find that mri_convert, without any -i?d or -o?d specifications does a fine job of reading the axial, unflipped data and it correctly outputs a coronal, flipped volume. So, my concern is how to output an axial unflipped volume correctly. I'm not getting the right answer using the -o?d flags. Please enlighten me ;-) Best, Darren PS, if this email gets through the mail server before the previous email (which has image attachments)...read the text of the previous email below and this message might make more sense :-) Darren Weber wrote: > > Hi, > > as best I can determine, the latest version of mri_convert is not using > the hdr.hist.orient field correctly. It is using orient=0 as if it is > RAS, when it must be LAS. it is also using the flipped values > (orient=3-5) incorrectly. > > Lets start with an Analyze volume with orient=0 (ie, the default Analyze > orientation in axial slices, with +X left, +Y anterior, +Z superior). A > display of this volume is attached as ucsf_ag_t1.jpg. Note how the > anatomical marker placed on the left cheek appears on the right hand > side of the axial slice (+X is LEFT, +Y is anterior, +Z is superior; > radiological orientation). The matlab tools I have for reading this > give the following: > > >> avw = avw_read('ucsf_ag/mri/analyze/ucsf_ag_t1') > > AVW_HDR_READ [v 1.10] > ...reading ieee-le Analyze format...done ( 0.02 sec). > > AVW_IMG_READ [v 1.9 ] > ...reading ieee-le Analyze int16 image format. > ...reading axial unflipped orientation > ...done (10.05 sec). > > > avw = > > hdr: [1x1 struct] > fileprefix: 'ucsf_ag/mri/analyze/ucsf_ag_t1' > img: [256x256x200 double] > > >> avw.hdr.hist.orient > > ans = > > 0 > > > > OK, now lets process this volume with mri_convert (to get from > 256x256x200 into 256x256x256, 1mm^3 voxels): > > Given that freesurfer prefers RAS volumes, we use the following command > on this Analyze volume: > > mri_convert -iid -1 0 0 -ijd 0 1 0 -ikd 0 0 1 analyze_in.img orig > > where the -iid indicates that the left-right direction is LAS rather > than RAS. This volume is then correctly oriented within the tkmedit > display. > > So now, we should be able to convert back from the orig volume into > Analyze, with the following command: > > mri_convert orig -oid -1 0 0 -ojd 0 1 0 -okd 0 0 1 analyze_out.img > > Again, we want to flip in X so we get back an LAS volume. However, > mri_convert is using the orient=3 (axial flipped) when it sees -oid -1 0 0. > > I stress that the flipped orient values (3-5) are not intended to > represent Neurological or Radiological orientation. The flipped values > are only designed to be used in movies (so they actually facilitate > speed of display for volumetic images on a 2D screen where the pixels > are updated from top to bottom of the screen). > > Even the default orientation is not correct. This, I think, is a > fundamental error of associating freesurfer RAS with Analyze orient=0. > The problem is that the orient=0 value is LAS, not RAS! For example, if > we specify the following: > > mri_convert ${sub}/mri/orig -oid 1 0 0 -ojd 0 1 0 -okd 0 0 1 > $sub/mri/analyze/${sub}_orig_axial_las.img >> ${sub}_mri_convert.log > > and then check the results with my matlab tools (mri_toolbox at > http://eeg.sf.net) we see the graphic attached in > ucsf_ag_orig_axial_ras.jpg (note that an anatomical marker was placed on > the LEFT cheek and according to orient=0, it should appear in > radiological orientation, with +X LEFT, but here it appears as +X RIGHT > - this is wrong!); here are the matlab commands: > > >> > >> avw = avw_read('ucsf_ag/mri/analyze/ucsf_ag_orig_axial_las') > > AVW_HDR_READ [v 1.10] > ...reading ieee-le Analyze format...done ( 0.02 sec). > > AVW_IMG_READ [v 1.9 ] > ...reading ieee-le Analyze uchar image format. > ...reading axial unflipped orientation > ...done (24.39 sec). > > > avw = > > hdr: [1x1 struct] > fileprefix: 'ucsf_ag/mri/analyze/ucsf_ag_orig_axial_las' > img: [256x256x256 double] > > >> avw.hdr.hist.orient > > ans = > > 0 > > > I may be missing something about how mri_convert has implemented the > allocation of values to the orient field of the header, but it appears > to me that it is not working in the manner described in the Analyze 7.5 > data format. I refer to the document available at: > > http://eeg.sourceforge.net/AnalyzeDirect_ANALYZEformat.pdf > > I did not see this problem in the previous version of mri_convert, so I > assume this is an initial attempt to implement handling of the orient > values in mri_convert. I'm not clear about how you have interpreted > this field or verified that mri_convert is working with it correctly. > Certainly, there is some inconsistency with my understanding of the > field and mri_convert implementation. I 'believe' that my reading and > implementation of the format documentation is correct. > > Best, Darren > > -- > Darren L. Weber, Postdoctoral Research Fellow, > Room 371-10, China Basin Landing, Dynamic Neuroimaging Laboratory, > Department of Radiology, University of California, San Francisco > 185 Berry Street, San Francisco, CA 94143-0946 > > Address for express mail/deliveries: > 185 Berry Street. Suite 350 > San Francisco, CA 94107 > > voice:(1) 415 353-9444 > fax: (1) 415 353-9421 > www: http://dnl.ucsf.edu/users/dweber > > > "People travel to wonder at the height of the mountains, > at the huge waves of the seas, at the long course of the rivers, > at the vast compass of the ocean, at the circular motion of the stars, > and yet they pass by themselves without wondering." > > St. Augustine, 354 430 > > ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > -- Best, Darren -- Darren L. Weber, Postdoctoral Research Fellow, Room 371-10, China Basin Landing, Dynamic Neuroimaging Laboratory, Department of Radiology, University of California, San Francisco 185 Berry Street, San Francisco, CA 94143-0946 Address for express mail/deliveries: 185 Berry Street. Suite 350 San Francisco, CA 94107 voice:(1) 415 353-9444 fax: (1) 415 353-9421 www: http://dnl.ucsf.edu/users/dweber "People travel to wonder at the height of the mountains, at the huge waves of the seas, at the long course of the rivers, at the vast compass of the ocean, at the circular motion of the stars, and yet they pass by themselves without wondering." St. Augustine, 354 430

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mris_sample_parc error
by Satrajit Ghosh 15 Mar '04

15 Mar '04

I am getting the following error when I run mris_sample_parc. Is this the proper command line? Thanks, Satra [labuser@... ~/subjects]$ mris_sample_parc ralasubj.01 lh parc1 parc reading parcellation volume from /speechlab/software/freesurfer/subjects/ralasubj.01/mri/parc1... reading input surface /speechlab/software/freesurfer/subjects/ralasubj.01/surf/lh.white... pass 1: 1588 segments changed pass 2: 407 segments changed pass 3: 182 segments changed pass 4: 181 segments changed pass 5: 177 segments changed pass 6: 180 segments changed pass 7: 177 segments changed pass 8: 180 segments changed pass 9: 177 segments changed pass 10: 180 segments changed pass 11: 177 segments changed writing annotation to lh.parc.annot... could not read annot file /speechlab/software/freesurfer/subjects/ralasubj.01/surf/../label/lh.lh.parc.annot No such file or directory

2 1

Mris_sample_parc
by Satrajit Ghosh 12 Mar '04

12 Mar '04

I can't find the mris_sample_parc command any longer in the distribution. Is this available somewhere or is there a substitute for it? Thanks, Satra

1 0

mri_normalize update
by Kevin Teich 11 Mar '04

11 Mar '04

The processing of control points in volume/surface creation in mri_normalize, used by csurf and recon-all, is broken for certain types of data in the 20040218 release. Please download one of these updates if you are having trouble: Darwin, 872KB: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mri_normalize-20040311-Darwin.tar… Linux, 1263KB: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mri_normalize-20040311-Linux.tar.… To unpack, move the file you download to your freesurfer/ directory, cd there, and run "tar zxvf <filename>". It will install bin/<OS>/mri_normalize. -- Kevin Teich

2 2

Tkmedit update for display transforms
by Kevin Teich 11 Mar '04

11 Mar '04

Display transforms in tkmedit are broken for certain types of data in the 20040218 release. Please download one of these updates if you are having trouble: Darwin, 1890KB: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/tkmedit-20040311-Darwin.tar.gz Linux, 1712KB: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/tkmedit-20040311-Linux.tar.gz To unpack, move the file you download to your freesurfer/ directory, cd there, and run "tar zxvf <filename>". It will install bin/<OS>/tkmedit and lib/tcl/tkmedit.tcl. -- Kevin Teich

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