Freesurfer

freesurfer@nmr.mgh.harvard.edu

2 participants
30050 discussions

having problem with motion correction.
by Tamara Knutsen 26 Mar '04

26 Mar '04

error is: >> >> >> >> >> >> ??? Undefined function or variable 'afni2bvol'. >> ------------------------------------------ ERROR: creating 011/fmc i'm just running: mc-sess -sf sf -df df at the command line (the files are correct, and the motion correction seems to start fine, but then it can't create these fmc files. any ideas? thanks tamara

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Snapshot of version
by Jonathan Wisco 25 Mar '04

25 Mar '04

Hi, I was wondering if I someone could send me a snapshot or pointer to the freesurfer recon tools for cortical inflation that was being used between Sept 2003 and Mar 2004. I suspect that the version changed somewhere in the middle of this time period and would like to analyze my data using the same version of freesurfer. Thanks, Jon --- Jonathan J. Wisco, Ph.D. Massachusetts General Hospital-NMR Center Building 149, 13th St., Mailcode 149-2301 Charlestown, MA 02129-2060 e-mail: jjwisco(a)nmr.mgh.harvard.edu tel: 617-851-8492 fax: 617-726-7422

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Re: [Freesurfer] is there any more documentation for mri_segment?
by Tamara Knutsen 25 Mar '04

25 Mar '04

you have to switch environments type use_dev (brings you to nmr-std-dev environment) and then type mri_segment -u and you will get the appropriate output. yes...documentation in general for all these things are indeed lacking. On Thu, 25 Mar 2004, Ned T. Sahin wrote: > Hi All, > > This thread brings up a more general point. It starts from the idea that > probably (just my guess) many people were surprised to find out that the > "-u" argument would yield more information about mri_segment. > > Let me make the strong assertion that well-behaved code should spit out > in the short version of feedback/documentation the method for getting > the long version. As in, when you just type in mri_segment, you should > get back a simple usage file that includes the flag you would need to > supply in order to get more usage information. > > How would a user know to try -u? It is only listed in the output you get > when you supply the flag. > > In fact, I just tried it: the -u flag does not give the output Brian > posted when most users give it. It only works if you have access to the > development environment. > > Furthermore, this is in the context of there being many standards for > how to evince extra online help from the various utilities used as part > of FreeSurfer and FS-FAST. > > In some cases, the flag is "-help" in others it is "--help" and in > others, apparently, it is "-u". When it is one, it is not the other - > for instance neither 'help' flag works with mri_segment. > > Of course I realize that much of this is historical - different > standards at different times, when various utilities were written. > Perhaps one is the chosen standard now. > > Any one person having to check and re-work all ~832 utilities, well, > would be quite annoyed. Especially because it is a mindless task. But, > could we utilize how mindless it is, and pawn it off in chunks to do in > spare moments to a fairly large net of developers at the Center? 5 > programs a week times 10 programmers would mean roughly 1 minute per > day, and yet the task would be done this summer. And of course it could > be much faster than that. The task, again, would be standardizing all > programs to give full info when one flag (say "-help") is supplied, and > making the simple usage prompt reflect this fact. > > The payoff is all users would be able to get the information below > immediately, rather than after 5 emails to the whole list, and in many > cases would be able to answer their own questions. > > Sorry for the rant, here. I hope it was useful, and the suggestion can > be implemented. > > > Thanks! > > > -ned t. sahin > > > > Brian T. Quinn wrote: > > > try the -u option for the following: > > > > -slope <float s> set the curvature slope (both n and p) > > -pslope <float p> set the curvature pslope (default=1.0) > > -nslope <float n> set the curvature nslope (default=1.0) > > -debug_voxel <int x y z> set voxel for debugging > > -auto automatically detect class statistics (default) > > -noauto don't automatically detect class statistics > > -log log to ./segment.dat > > -keep keep wm edits. maintains all values of 0 and 255 > > -ghi, -gray_hi <int h> set the gray matter high limit > > (default=100.000) > > -wlo, -wm_low <int l> set the white matter low limit > > (default=90.000) > > -whi, -wm_hi <int h> set the white matter high limit > > (default=125.000) > > -nseg <int n> thicken the n largest thin strands (default=20) > > -thicken toggle thickening step (default=ON) > > -fillbg toggle filling of the basal ganglia > > (default=OFF) > > -fillv toggle filling of the ventricles (default=OFF) > > -b <float s> set blur sigma (default=0.25) > > -n <int i> set # iterations of border classification > > (default=1) > > -t <int t> set limit to thin strands in mm (default=4) > > -v verbose > > -p <float p> set % threshold (default=0.80) > > -x <filename> extract options from filename > > -w <int w> set wsize (default=11) > > -u usage > > > > good luck, > > -- > > brian t. quinn > > > > > > On Thu, 25 Mar 2004, Tamara Knutsen wrote: > > > > > >>this is all i find: > >> > >>[whatever:ben1] (nmr-std-env) mri_segment > >>usage: mri_segment <input volume> <output volume> > >> > >>thanks! > >> > >> > >>_______________________________________________ > >>Freesurfer mailing list > >>Freesurfer(a)nmr.mgh.harvard.edu > >>http://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > http://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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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

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